bluuebunny/crossref_metadata_2025 huggingface dataset:
Circular Stapled Technique Versus Modified Collard Technique for Cervical Esophagogastric Anastomosis After Esophagectomy
Authors: Hosoi Takahiro , Abe Tetsuya , Higaki Eiji , Fujieda Hironori , Nagao Takuya , Ito Seiji , Komori Koji , Iwase Madoka , Oze Isao , Shimizu Yasuhiro
Published: August 2021

Objective:

This study was performed to investigate the efficacy of the modified Collard (MC) technique for reducing anastomotic stricture after esophagectomy compared with the circular stapled (CS) technique.

Summary Background Data:

The currently available techniques of anastomosis after esophagectomy are associated with a significant risk of anasto-motic complications. However, the optimal anastomotic technique after esophagectomy has not yet been established.

Methods:

We randomly allocated patients to either the CS group or the MC group. The primary endpoint was the incidence of anastomotic stricture. The secondary endpoints included the incidence of postoperative complications (including anastomotic leakage) and quality of life (QoL). All anastomoses were performed after indocyanine green evaluation for objective homogeni-zation of blood flow to the gastric conduit between the 2 techniques.

Results:

Among 100 randomized patients (CS group, n = 50; MC group, n = 50), anastomotic strictures were observed in 18 (42%) patients in the CS group and in no patients in the MC group. There were no significant between-group differences in anastomotic leakage (CS group, 7% vs MC group, 8%; P = 0.94). Quality of life domains of dysphagia and choking when swallowing at 3 months after surgery were significantly better in the MC group than in the CS group.

Conclusions:

The MC technique reduces the incidence of anastomotic stricture and improves postoperative quality of life. Furthermore, the incidence of anastomotic leakage is comparable between the 2 techniques based on accurate comparison under objective homogenization of the gastric conduit condition.
Three-dimensional volume-rendered computed tomography application for follow-up fracture healing and volume measurements pre–surgical rib fixation and post–surgical rib fixation
Authors: Campbell Don , Arnold Nicholas , Wake Elizabeth , Grieve John , Provenzano Sylvio , Wullschleger Martin , Patel Bhavik
Published: August 2021

BACKGROUND

Surgical rib fixation (SRF) is being used increasingly in trauma centers for stabilization of chest wall injuries, in line with new and evolving surgical techniques. Our institution has developed a pathway for the management of chest wall injuries and SRF, which includes a follow-up low-volume, noncontrast computed tomography (CT) scan at 12 months.

METHODS

This study was a single-center retrospective study conducted on 25 consecutive patients who underwent SRF between February 2019 and February 2020. All CT measurements were done by a CT radiographer under the supervision of a board-certified radiologist and included the use of three-dimensional volume-rendered images.

RESULTS

There were no patients with SRF who experienced hardware failure at 12 months in either flail or nonflail groups. For fractured ribs treated with SRF, complete or partial union occurred in 75 of 76 ribs plated (98.7%). The median ratio for improvement in lung volumes was 1.71 for flail SRF and 1.69 for nonflail SRF in our study.

CONCLUSION

Three-dimensional volume-rendered CT at 12 months post-SRF showed good alignment (no hardware failure) and fracture healing of fixed ribs in both flail and nonflail groups. Lung volumes also improved pre-SRF and post-SRF for both flail and nonflail patients. More studies are needed to define how the pattern of rib fracture healing of fixed and nonfixed ribs affects lung volumes.

LEVEL OF EVIDENCE

Therapeutic, Level V.
Delayed Opsoclonus–Myoclonus Syndrome After Ovarian Teratoma Resection
Authors: Jones Andrea A. , Chen Tychicus
Published: August 2021

Opsoclonus–myoclonus syndrome (OMS) is a rare syndrome characterized by opsoclonus, which is irregular, spontaneous, multivectorial saccadic eye movements, along with diffuse or focal myoclonus and sometimes ataxia. OMS is associated with paraneoplastic etiologies in 20%–40% of cases, with small-cell lung and breast cancers the most common associated primary neoplasms in adults, whereas neuroblastoma is more common in children and ovarian teratoma may occur in women younger than 30 years. Onconeural antibodies are often not identified. In existing literature, paraneoplastic OMS precedes identification of the neoplasm, and neurological recovery depends on treatment of the underlying cancer. We describe a 27-year-old woman with the delayed onset of OMS one month after resection of ovarian teratoma, likely due to immune trigger from antigen exposure at the time of resection. She was treated with intravenous methylprednisolone, immunoglobulins, and eventually rituximab with resolution of her symptoms. Identification of OMS after tumor resection and prompt immunotherapy are critical for neurologic recovery. At 30-month follow-up, this patient had not experienced recurrence of OMS.
Etiology and Outcomes of Acquired Pediatric Sixth Nerve Palsies
Authors: Chang Melinda Y. , Borchert Mark S.
Published: August 2021

Background:

Acquired sixth nerve (CN6) palsies in children may be benign or associated with an underlying neurologic condition. In children who presented with isolated (no associated neurologic or ophthalmic symptoms or signs) CN6 palsies, the rate of newly diagnosed neurologic disorders (such as tumors) is unclear. Moreover, the factors associated with spontaneous resolution and amblyopia in children with acquired CN6 palsies are unknown.

Methods:

We retrospectively reviewed the charts of all children younger than 18 years diagnosed with CN6 palsy at our institution from 2010 to 2020. We recorded ophthalmologic and neurologic history and examination findings, neuroimaging results, etiology of CN6 palsy, and outcomes including spontaneous resolution and amblyopia. We assessed etiologies of isolated and nonisolated CN6 palsies as well as frequency and factors associated with spontaneous resolution and amblyopia (in children ≤7 years).

Results:

One hundred seventy-two children met inclusion criteria. Twenty CN6 palsies (12%) were isolated at presentation. Most isolated cases were presumed postviral or postvaccination (50%) or idiopathic (30%), but 2 cases (10%) were associated with newly diagnosed tumors. Spontaneous resolution occurred in 59% of CN6 palsies at a median of 12.3 weeks and was associated with older age (P = 0.03) and nontumor etiology (P = 0.006). Amblyopia developed in 18% of children at risk, exclusively in those with anisometropia, pre-existing strabismus, or younger than 12 months.

Conclusions:

Our findings and chart reviews suggest that approximately 10% of isolated acquired pediatric CN6 palsies are associated with a newly diagnosed brain tumor. This risk must be discussed with parents when considering immediate vs delayed neuroimaging. In addition, infants and children ≤7 years with secondary amblyogenic risk factors (anisometropia or pre-existing strabismus) require close follow-up to monitor and treat amblyopia.
The microvascular hypothesis underlying neurologic manifestations of long COVID-19 and possible therapeutic strategies
Authors:   Research Accessibility Team (RAT)
Published: August 2021

With the ongoing distribution of the coronavirus disease (COVID) vaccines, the pandemic of our age is ending, leaving the world to deal with its well-documented aftereffects. Long COVID comprises a variety of symptoms, of which the neurological component prevails. The most permeating theory on the genesis of these symptoms builds upon the development of microvascular dysfunction similar to that seen in numerous vascular diseases such as diabetes. This can occur through the peripheral activation of angiotensin-converting enzyme 2 receptors, or through exacerbations of pro-inflammatory cytokines that can remain in circulation even after the infection diminishes. Several drugs have been identified to act on the neurovascular unit to promote repair, such as gliptins, and others. They also succeeded in improving neurologic outcome in diabetic patients. The repurposing of such drugs for treatment of long COVID-19 can possibly shorten the time to recovery of long COVID-19 syndrome.
Course-based Undergraduate Research Module for Enzyme Discovery Using Protein Structure Prediction
Authors: Kelz Jessica I. , Takahashi Gemma R. , Safizadeh Fatemeh , Farahmand Vesta , Crosby Marquise G. , Uribe Jose Luis , Kim Suhn H. , Sprague-Piercy Marc A. , Diessner Elizabeth M. , Norton-Baker Brenna , Damo Steven M. , Martin Rachel W. , Kadandale Pavan
Published: August 2021

A major challenge for science educators is teaching foundational concepts while introducing their students to current research. Here we describe an active learning module developed to teach protein structure fundamentals while supporting ongoing research in enzyme discovery. It can be readily implemented in both entry-level and upper-division college biochemistry or biophysics courses. Pre-activity lectures introduced fundamentals of protein secondary structure and provided context for the research projects, while a homework assignment familiarized students with 3D visualization of biomolecules using UCSF Chimera, a free protein structure viewer. The activity is an online survey in which students compare structure elements in papain, a well-characterized cysteine protease fromCarica papaya, to novel homologous proteases identified from the genomes of an extremophilic microbe (Halanaerobium praevalens) and two carnivorous plants (Drosera capensisandCephalotus follicularis). Students were then able to identify, with varying levels of accuracy, a number of structural features in cysteine proteases that could expedite the identification of novel or biochemically interesting cysteine proteases for experimental validation in a university laboratory. Student responses to a post-activity survey were largely positive and constructive, describing points in the activity that could be improved and indicating that the activity helped them learn about protein structure.
Apoplastic class III peroxidases PRX62 and PRX69 regulate ROS-homeostasis and cell wall associated extensins linked to root hair growth at low-temperature in Arabidopsis thaliana
Authors: Pacheco Javier Martinez , Ranocha Philippe , Kasulin Luciana , Fusari Corina M. , Servi Lucas , Ferrero Lucía , Gabarain Victoria Berdion , Peralta Juan Manuel , Borassi Cecilia , Marzol Eliana , Rodríguez-Garcia Diana Rosa , Rondón Guerrero Yossmayer del Carmen , Sardoy Mariana Carignani , Botto Javier , Meneses Claudio , Ariel Federico , Petrillo Ezequiel , Dunand Christophe , Estevez José M.
Published: August 2021

Root Hairs (RHs) growth is highly influenced by endogenous as well as by external environmental signals that coordinately regulate its final cell size. RHs actively expand the root surface responsible for nutrient uptake and water absorption. We have recently determined that RH growth was unexpectedly boosted when Arabidopsis thaliana seedlings are cultivated at low temperatures. It was proposed that RH growth plasticity in response to low temperature was linked to a reduced nutrient availability in the media. Here, we explored the molecular basis of this strong RH growth response by using the Genome Wide Association Studies (GWAS) approach on Arabidopsis thaliana natural accessions. We identified the poorly characterized PEROXIDASE 62 (PRX62) as a key protein triggering this conditional growth under a moderate low-temperature stress. In addition, we identified the related protein PRX69 as an important factor in this developmental process. The prx62 prx69 double mutant and the PRX62 and PRX69 over-expressing lines showed contrasting RH phenotypes, peroxidase activities and cyt/apoReactive Oxygen Species (ROS) levels. Strikingly, a cell wall protein extensin (EXT) reporter revealed the effect of peroxidase activity on the EXT cell wall association at 10°C in the RH apical zone. EXT cell wall insolubilization was enhanced at 10°C, which was completely abolished under the PRX inhibitor salicylhydroxamic acid (SHAM) treatment. Finally, we demonstrated that the Root Hair defective 6-like 4 (RSL4) bHLH family transcription factor directly controls the expression of PRX69. Collectively, our results indicate that both PRX62 and PRX69 are key apoplastic PRXs that modulate ROS-homeostasis and cell wall EXT-insolubilization linked to RH elongation at low-temperature.
The ataxia protein sacsin is required for integrin trafficking and synaptic organization
Authors: Romano Lisa E.L. , Aw Wen Yih , Hixson Kathryn M. , Novoselova Tatiana V. , Havener Tammy M. , Howell Stefanie , Hall Charlotte L , Xing Lei , Beri Josh , Nethisinghe Suran , Perna Laura , Hatimy Abubakar , Chioccioli Altadonna Ginevra , Graves Lee M. , Herring Laura E. , Hickey Anthony J. , Thalassinos Konstantinos , Chapple J. Paul , Wolter Justin M.
Published: August 2021

Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) is caused by mutations in SACS, which manifest as a childhood-onset cerebellar ataxia. Cellular ARSACS phenotypes include mitochondrial dysfunction, intermediate filament (IF) disorganization, and loss of Purkinje neurons. It is unclear how the loss of SACS causes these deficits, or why they manifest as cerebellar ataxia. We employed a multi-omics approach to characterize molecular and cellular deficiencies in SACS knockout (KO) cells. We identified alterations in microtubule structure and dynamics, protein trafficking, and mislocalization of synaptic and focal adhesion proteins. Targeting PTEN, a negative regulator of focal adhesions, rescued several cellular phenotypes in SACS KO cells. We found sacsin interacts with proteins implicated in vesicle transport, including HSP proteins, and interactions between structural and cell adhesion proteins were diminished in SACS KO cells. In all, this study suggests that trafficking and localization of synaptic adhesion proteins is a causal molecular deficiency in ARSACS.
Bacterial glycyl tRNA synthetase offers glimpses of ancestral protein topologies
Authors: Dimas-Torres Jorge-Uriel , Rodríguez-Hernández Annia , Valencia-Sánchez Marco Igor , Campos-Chávez Eduardo , Godínez-López Victoria , Rodríguez-Chamorro Daniel-Eduardo , Grøtli Morten , Fleming Cassandra , Hernández-González Adriana , Arciniega Marcelino , Torres-Larios Alfredo
Published: August 2021

Aminoacyl tRNA synthetases (aaRSs) are among the proposed proteins present in the Last Universal Common Ancestor (LUCA). There are two types of glycyl tRNA synthetases (GlyRSs), from which the archaeal-eukaryal type is the one suggested to be present in LUCA. Here we solved the crystal structure of a complete bacterial glycyl tRNA synthetase (bacGlyRS) and show that indeed, bacGlyRS carries several structural signals that point it at the origin of all aaRSs. Furthermore, if bacGlyRS is ancestral, it should help to build a reliable Tree of Life (ToL). Given the modular nature of protein evolution, we used only two sub-domain segments with duplicated ancestral topologies, no detected orthologs and an assumed limited horizontal gene transfer (HGT). These motifs correspond to the non-specific RNA binding regions of contemporary bacGlyRS, archaeal CCA-adding enzyme (arch-CCAadd), and eukaryotic rRNA processing enzyme (euk-rRNA). The calculated, rooted bacterial ToL agrees with several phyla relationships unaccounted by the available trees.
Mutations that adapt SARS-CoV-2 to mustelid hosts do not increase fitness in the human airway
Authors: Zhou Jie , Peacock Thomas P. , Brown Jonathan C. , Goldhill Daniel H. , Elrefaey Ahmed M.E. , Penrice-Randal Rebekah , Cowton Vanessa M. , Lorenzo Giuditta De , Furnon Wilhelm , Harvey William T. , Kugathasan Ruthiran , Frise Rebecca , Baillon Laury , Lassaunière Ria , Thakur Nazia , Gallo Giulia , Goldswain Hannah , Donovan-Banfield I’ah , Dong Xiaofeng , Randle Nadine P. , Sweeney Fiachra , Glynn Martha C. , Quantrill Jessica L. , McKay Paul F. , Patel Arvind H. , Palmarini Massimo , Hiscox Julian A. , Bailey Dalan , Barclay Wendy S.
Published: August 2021

SARS-CoV-2 has a broad mammalian species tropism infecting humans, cats, dogs and farmed mink. Since the start of the 2019 pandemic several reverse zoonotic outbreaks of SARS-CoV-2 have occurred in mink, one of which reinfected humans and caused a cluster of infections in Denmark. Here we investigate the molecular basis of mink and ferret adaptation and demonstrate the spike mutations Y453F, F486L, and N501T all specifically adapt SARS-CoV-2 to use mustelid ACE2. Furthermore, we risk assess these mutations and conclude mink-adapted viruses are unlikely to pose an increased threat to humans, as Y453F attenuates the virus replication in human cells and all 3 mink-adaptations have minimal antigenic impact. Finally, we show that certain SARS-CoV-2 variants emerging from circulation in humans may naturally have a greater propensity to infect mustelid hosts and therefore these species should continue to be surveyed for reverse zoonotic infections.
Progerin-Expressing Endothelial Cells are Unable to Adapt to Shear Stress
Authors: Danielsson Brooke E. , Peters Hannah C. , Bathula Kranthi , Spear Lindsay M. , Noll Natalie A. , Dahl Kris N. , Conway Daniel E.
Published: August 2021

Hutchinson-Gilford Progeria Syndrome (HGPS) is a rare premature aging disease caused by a single-point mutation in the lamin A gene, resulting in a truncated and farnesylated form of lamin A. This mutant lamin A protein, known as progerin, accumulates at the periphery of the nuclear lamina, resulting in both an abnormal nuclear morphology and nuclear stiffening. HGPS patients experience rapid onset of atherosclerosis, with death from heart attack or stroke as teenagers. Progerin expression has been shown to cause dysfunction in both vascular smooth muscle cells and endothelial cells (ECs). In this study we examined how progerin-expressing ECs adapt to fluid shear stress, the principal mechanical force from blood flow. We compared the response to shear stress for progerin-expressing, wild-type lamin A overexpressing, and control ECs to physiological levels of fluid shear stress. Additionally, we also knocked down ZMPSTE24 in ECs, which results in increased farnesylation of lamin A and similar phenotypes to HGPS. Our results showed that ECs either expressing progerin or with ZMPSTE24 knockdown were unable to adapt to shear stress, experiencing significant cell loss at a longer duration of exposure to shear stress (3 days). ECs overexpressing wild-type lamin A also exhibited similar impairments in adaptation to shear stress, including similar levels of cell loss. Quantification of nuclear morphology showed that progerin-expressing ECs had similar nuclear abnormalities in both static and shear conditions. Treatment of progerin-expressing cells and ZMPSTE24 KD cells with lonafarnib and methystat, drugs previously shown to improve HGPS nuclear morphology, resulted in improvements in adaptation to shear stress. Additionally, pre-alignment of cells to shear stress prior to progerin-expression prevented cell loss. Our results demonstrate that changes in nuclear lamins can affect the ability of EC to properly adapt to shear stress.
Interferon-γ Increases Sensitivity to Chemotherapy and Provides Immunotherapy Targets in Models of Metastatic Castration-Resistant Prostate Cancer
Authors: Korentzelos Dimitrios , Wells Alan , Clark Amanda M.
Published: August 2021

Interferon-γ (IFNγ) is a cytokine with limited evidence of benefit in cancer clinical trials to date. However, it could potentially play a role in potentiating anti-tumor immunity in the immunologically “cold” metastatic castration-resistant prostate cancer (mCRPC) by inducing antigen presentation pathways and concurrently providing targets for immune checkpoint blockade therapy. Moreover, it could additionally increase sensitivity to chemotherapy based on its pleiotropic effects on cell phenotype. Here, we show that IFNγ treatment induced expression of major histocompatibility class-I (MHC-I) genes and PD-L1 in prostate cancer cells in vitro. Furthermore, IFNγ treatment led to a decrease in E-cadherin expression with a consequent increase in sensitivity to chemotherapy in vitro. In an in vivo murine tumor model of spontaneous metastatic prostate cancer, IFNγ systemic pretreatment upregulated the expression of HLA-A and decreased E-cadherin expression in the primary tumor, and more importantly in the metastatic site led to increased apoptosis and limited micrometastases in combination with paclitaxel treatment compared to diffuse metastatic disease in control and monotherapy treatment groups. These findings suggest that IFNγ may be useful in combinatorial regimens to induce sensitivity to immunotherapy and chemotherapy in hepatic metastases of mCRPC.
FKBPL and FKBP8 regulate DLK degradation and neuronal responses to axon injury
Authors: Lee Bohm , Oh Yeonsoo , Cho Eunhye , DiAntonio Aaron , Cavalli Valeria , Shin Jung Eun , Cho Yongcheol
Published: August 2021

DLK is a key regulator of axon regeneration and degeneration in response to neuronal injury. To understand the molecular mechanisms controlling the DLK function, we performed yeast two-hybrid screening analysis and identified FKBPL as a DLK-binding protein that bound to the kinase domain and inhibited the kinase enzymatic activity of DLK. FKBPL regulated DLK stability through ubiquitin-dependent DLK degradation. We tested other members in the FKBP protein family and found that FKBP8 also induced DLK degradation as FKBPL did. We found that Lysine 271 residue in the kinase domain of DLK was a major site of ubiquitination and SUMO3-conjugation and responsible for FKBP8-mediated degradation. In vivo overexpression of FKBP8 delayed progression of axon degeneration and neuronal death following axotomy in sciatic and optic nerves, respectively, although axon regeneration efficiency was not enhanced. This research identified FKBPL and FKBP8 as new DLK-interacting proteins that regulated DLK stability by MG-132 or bafilomycin A1-sensitive protein degradation.
Subtype specific responses in hKv7.4 and hKv7.5 channels to polyunsaturated fatty acids
Authors: Frampton Damon J A , Nikesjö Johan , Liin Sara I
Published: August 2021

The KV7.4 and KV7.5 subtypes of voltage-gated potassium channels are expressed in several tissues where they play a role in physiological processes such as sound amplification in the cochlea and adjusting vascular smooth muscle tone. Therefore, the mechanisms that regulate KV7.4 and KV7.5 channel function are of interest. Here, we study the effect of polyunsaturated fatty acids (PUFAs) on human KV7.4 and KV7.5 channels expressed inXenopusoocytes. We report that KV7.5 is activated by PUFAs, which shift the V50of the conductanceversusvoltage (G(V)) curve towards more negative voltages. This response depends on the charge of the head group as an uncharged PUFA analogue has no effect and a positively charged PUFA analogue induces positive V50shifts. In contrast, we find that the KV7.4 channel is inhibited by PUFAs, which shift V50towards more positive voltages. No effect on V50of KV7.4 is observed by an uncharged or a positively charged PUFA analogue. Oocytes co-expressing KV7.4 and KV7.5 display an intermediate response to PUFAs. Altogether, the KV7.5 channel’s response to PUFAs is like that previously observed in KV7.1-7.3 channels, whereas the KV7.4 channel response is opposite, revealing subtype specific responses to PUFAs.
XRN2-mediated regulation of tumor suppressor microRNAs is of critical pathophysiological significance in Humans
Authors: Nalawade Rohit , Chowdhury Tamoghna , Chatterjee Saibal
Published: August 2021

MicroRNAs (miRNAs) are critical regulators of diverse developmental and physiological processes, and they themselves get regulated both at the level of biogenesis and turnover. We demonstrate that the ribonuclease XRN2 can degrade the mature forms of certain let-7 family members in multiple human cancer cell lines, without affecting their precursors. XRN2 also affects the accumulation of several other tumor suppressor miRNAs known to play important roles in cancer metabolism. XRN2 depletion results in a reduction in the expression of many oncogenes and diminishes the proliferative and metastatic potential of cancer cellsin vitro. These experimental cancer cells also show reduced capacity to form tumors in mice and regress over time. The clinical relevance of these observations is further verified in tumour transcriptomics data from public RNA-sequencing datasets, whereXRN2mRNA expression is inversely correlated with the levels of a large number of miRNAs, including let-7 members, and highXRN2mRNA levels are associated with poor survival in hepatocellular carcinoma, lung adenocarcinoma, and glioblastoma. We demonstrate that the miRNA is released by an as-yet unidentified proteinaceous ‘miRNA release factor’ from the grasp of Argonaute before its degradation, which is more abundant in the nuclear fraction. Our analyses of the patient-derived transcriptomics data also show that XRN2, via its regulation of let-7, affects multiple pathways in a consistent manner across epithelial and glial cell lineages, and thus, is of critical pathophysiological significance.
Heterotypic Assembly Mechanism Regulates CHIP E3 Ligase Activity
Authors: Das Aniruddha , Thapa Pankaj , Santiago Ulises , Shanmugam Nilesh , Banasiak Katarzyna , Dabrowska Katarzyna , Nolte Hendrik , Szulc Natalia A. , Gathungu Rose M. , Cysewski Dominik , Krüger Marcus , Dadlez Michal , Nowotny Marcin , Camacho Carlos J. , Hoppe Thorsten , Pokrzywa Wojciech
Published: August 2021

The E3 ubiquitin ligases CHIP/CHN-1 and UFD-2 team up to accelerate ubiquitin chain formation. However, it remained largely unclear how the high processivity of this E3 set is achieved. Here we studied the molecular mechanism and function of the CHN-1/UFD-2 complex in Caenorhabditis elegans. Our data show that UFD-2 binding promotes the cooperation between CHN-1 and ubiquitin-conjugating E2 enzymes by stabilizing the CHN-1 U-box dimer. The HSP-1 chaperone outcompetes UFD-2 for CHN-1 binding and promotes the auto-inhibited CHN-1 state by acting on the conserved position of the U-box domain. The interaction with UFD-2 enables CHN-1 to efficiently ubiquitinate S-Adenosylhomocysteinase (AHCY-1), an enzyme crucial for lipid metabolism. Our results define the molecular mechanism underlying the synergistic cooperation of CHN-1 and UFD-2 in substrate ubiquitylation.

HIGHLIGHTS

E3 ligase UFD-2 stimulates ubiquitylation activity of CHIP/CHN-1

UFD-2 binding promotes dimerization of CHIP/CHN-1 U-box domains and utilization of E2 enzymes

HSP70/HSP-1 by latching the U-box and TPR domains stabilizes the autoinhibitory state of CHIP/CHN-1, limiting interactions with E2s and UFD-2

Assembly with UFD-2 enables CHIP/CHN-1 to regulate lipid metabolism by ubiquitylation of S-Adenosylhomocysteinase
Genetic Characterization and Curation of Diploid A-Genome Wheat Species
Authors: Adhikari Laxman , Raupp John , Wu Shuangye , Wilson Duane , Evers Byron , Koo Dal-Hoe , Singh Narinder , Friebe Bernd , Poland Jesse
Published: August 2021

The A-genome diploid wheats represent the earliest domesticated and cultivated wheat species in the Fertile Crescent and the donor of the wheat A sub-genome. The A-genome species encompass the cultivated einkorn (Triticum. monococcum L. subsp. monococcum), wild einkorn (T. monococcum L. subsp. aegilopoides (Link) Thell.) and T. urartu. We evaluated the collection of 930 accessions in the Wheat Genetics Resource Center (WGRC), using genotyping-by-sequencing (GBS) and identified 13,089 curated SNPs. Genomic analysis detected misclassified and duplicated accessions with most duplicates originated from the same or a nearby locations. About 56% (n = 520) of the WGRC A-genome species collections were duplicates supporting the need for genomic characterization for effective curation and maintenance of these collections. Population structure analysis confirmed the morphology-based classifications of the accessions and reflected the species geographic distributions. We also showed that the T. urartu as the closest A-genome diploid to wheat through phylogenetic analysis. Population analysis within the wild einkorn group showed three genetically distinct clusters, which corresponded with wild einkorn races α, β, and γ described previously. The T. monococcum genome-wide FST scan identified candidate genomic regions harboring domestication selection signature (Btr1) on the short arm of chromosome 3Am at ~ 70 Mb. We established A-genome core set (79 accessions) based on allelic diversity, geographical distribution, and available phenotypic data. The individual species core set maintained at least 80% of allelic variants in the A-genome collection and constitute a valuable genetic resource to improve wheat and domesticated einkorn in breeding programs.

One-sentence summary

Genotyping of gene bank collections of diploid A-genome relatives of wheat uncovered relatively higher genetic diversity and unique evolutionary relationships which gives insight to the effective use of these germplasm for wheat improvement.
High-Spatiotemporal-Resolution Nanopore Sequencing of SARS-CoV-2 and Host Cell RNAs
Authors: Tombácz Dóra , Dörmő Ákos , Gulyás Gábor , Csabai Zsolt , Prazsák István , Kakuk Balázs , Harangozó Ákos , Jankovics István , Dénes Béla , Boldogkői Zsolt
Published: August 2021

Recent studies have disclosed the genome, transcriptome and epigenetic compositions of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the effect of viral infection on gene expression of the host cells. It has been demonstrated that, besides the major canonical transcripts, the viral genome also codes for non-canonical RNA molecules. While the structural characterizations have revealed a detailed transcriptomic architecture of the virus, the kinetic studies provided poor and often misleading results on the dynamics of both the viral and host transcripts due to the low temporal resolution of the infection event and the low virus/cell ratio (MOI=0.1) applied for the infection. In this study, we used direct cDNA and direct RNA nanopore sequencings for the generation of high-coverage, high-temporal-resolution transcriptomic datasets on SARS-CoV-2 and on primate host cells infected with a high virus titer (MOI=5). Sixteen sampling time points ranging from 1 to 96h with a varying time resolution and three biological replicates were used in the experiment for both the infected and the non-infected cells.
Vps54 regulates lifespan and locomotor behavior in adult Drosophila melanogaster
Authors: Wilkinson Emily C. , Starke Emily L. , Barbee Scott A.
Published: August 2021

Vps54 is an integral subunit of the Golgi-associated retrograde protein (GARP) complex, which is involved in tethering endosome-derived vesicles to the trans-Golgi network (TGN). A destabilizing missense mutation in Vps54 causes the age-progressive motor neuron (MN) degeneration, muscle weakness, and muscle atrophy observed in the wobbler mouse, an established animal model for human MN disease. It is currently unclear how the disruption of Vps54, and thereby the GARP complex, leads to MN and muscle phenotypes. To develop a new tool to address this question, we have created an analogous model in Drosophila by generating novel loss-of-function alleles of the fly Vps54 ortholog (scattered/scat). We find that null scat mutant adults are viable but have a significantly shortened lifespan. Like phenotypes observed in the wobbler mouse, we show that scat mutant adults are male sterile and have significantly reduced body size and muscle area. Moreover, we demonstrate that scat mutant adults have significant age-progressive defects in locomotor function. Interestingly, we see sexually dimorphic effects, with scat mutant adult females exhibiting significantly stronger phenotypes. Finally, we show that scat interacts genetically with rab11 in MNs to control age-progressive muscle atrophy in adults. Together, these data suggest that scat mutant flies share mutant phenotypes with the wobbler mouse and may serve as a new genetic model system to study the cellular and molecular mechanisms underlying MN disease.
Development of a universal nanobody-binding Fab module for fiducial-assisted cryo-EM studies of membrane proteins
Authors: Bloch Joël S. , Mukherjee Somnath , Kowal Julia , Filippova Ekaterina V. , Niederer Martina , Pardon Els , Steyaert Jan , Kossiakoff Anthony A. , Locher Kaspar P.
Published: August 2021

With conformation-specific nanobodies being used for a wide range of structural, biochemical, and cell biological applications, there is a demand for antigen-binding fragments (Fabs) that specifically and tightly bind these nanobodies without disturbing the nanobody-target protein interaction. Here we describe the development of a synthetic Fab (termed NabFab) that binds the scaffold of an alpaca-derived nanobody with picomolar affinity. We demonstrate that upon CDR grafting onto this parent nanobody scaffold, nanobodies recognizing diverse target proteins and derived from llama or camel can cross-react with NabFab without loss of affinity. Using NabFab as a fiducial and size enhancer (50 kDa), we determined the high-resolution cryo-EM structures of nanobody-bound VcNorM and ScaDMT, both small membrane proteins of ~50 kDa. Using an additional anti-Fab nanobody further facillitated reliable initial 3D structure determination from small cryo-EM test datasets. Given that NabFab is of synthetic origin, humanized, and can be conveniently expressed in E. coli in large amounts, it may not only be useful for structural biology, but also for biomedical applications.
Stable antibiotic resistance and rapid human adaptation in livestock-associated MRSA
Authors: Matuszewska Marta , Murray Gemma G. R. , Ba Xiaoliang , Wood Rhiannon , Holmes Mark A. , Weinert Lucy A.
Published: August 2021

Mobile genetic elements (MGEs) are agents of horizontal gene transfer in bacteria, but can also be vertically inherited by daughter cells. Establishing the dynamics that led to contemporary patterns of MGEs in bacterial genomes is central to predicting the emergence and evolution of novel and resistant pathogens. Methicillin-resistant Staphylococcus aureus (MRSA) clonal-complex (CC) 398 is the dominant MRSA in European livestock and a growing cause of human infections. Previous studies have identified three categories of MGEs whose presence or absence distinguishes livestock-associated CC398 from a closely related and less antibiotic-resistant human-associated population. Here we fully characterise the evolutionary dynamics of these MGEs using a collection of 1,180 CC398 genomes, sampled from livestock and humans, over 27 years. We find that the emergence of livestock-associated CC398 coincided with the acquisition of a Tn916 transposon carrying a tetracycline resistance gene, which has been stably inherited for 57 years. This was followed by the acquisition of a type V SCCmec that carries methicillin, tetracycline and heavy metal resistance genes, which has been maintained for 35 years, with occasional truncations and replacements with type IV SCCmec. In contrast, a class of prophages that carry a human immune evasion gene cluster and that are largely absent from livestock-associated CC398, have been repeatedly gained and lost in both human- and livestock-associated CC398. These contrasting dynamics mean that when livestock-associated MRSA is transmitted to humans, adaptation to the human host outpaces loss of antibiotic resistance. In addition, the stable inheritance of resistance-associated MGEs suggests that the impact of ongoing reductions in antibiotic and zinc oxide use in European farms on livestock-associated MRSA will be slow to be realised.
Interactomic analysis reveals a new homeostatic role for the HIV restriction factor TRIM5α in mitophagy
Authors: Saha Bhaskar , Salemi Michelle , Williams Geneva L , Paffett Michael L , Phinney Brett , Mandell Michael A
Published: August 2021

The protein TRIM5α has multiple roles in anti-retroviral defense, but the mechanisms underlying TRIM5α action are unclear. Here, we used an APEX2-based proteomics approach to identify TRIM5α-interacting proteins. Analysis of the TRIM5α interactome found proteins participating in a wide variety of cellular functions including regulating antiviral signaling pathways. We used this data set to uncover a novel role for TRIM5α in mitophagy, an autophagy-based mode of mitochondrial quality control that is compromised in multiple human diseases. Mitochondrial damage triggered the relocalization of TRIM5α to ER-mitochondria contact sites where TRIM5α colocalized with markers of autophagy initiation and autophagosome biogenesis. Furthermore, we found that TRIM5α knockout attenuated both Parkin-dependent and Parkin-independent mitophagy by preventing the recruitment of autophagy regulators FIP200 and ATG13 to unhealthy mitochondria. Finally, TRIM5α knockout cells showed reduced mitochondrial function under basal conditions and were more susceptible to uncontrolled immune activation and cell death in response to mitochondrial damage than were wild type cells. Taken together, our studies have identified a homeostatic role for a protein previously recognized exclusively for its antiviral actions.
Machine learning enables discovery of DNA-carbon nanotube sensors for serotonin
Authors: Kelich Payam , Jeong Sanghwa , Navarro Nicole , Adams Jaquesta , Sun Xiaoqi , Zhao Huanhuan , Landry Markita P. , Vuković Lela
Published: August 2021

DNA-wrapped single walled carbon nanotube (SWNT) conjugates have remarkable optical properties leading to their use in biosensing and imaging applications. A critical limitation in the development of DNA-SWNT sensors is the current inability to predict unique DNA sequences that confer a strong analyte-specific optical response to these sensors. Here, near-infrared (nIR) fluorescence response datasets for ~100 DNA-SWNT conjugates, narrowed down by a selective evolution protocol starting from a pool of ~1010 unique DNA-SWNT candidates, are used to train machine learning (ML) models to predict new unique DNA sequences with strong optical response to neurotransmitter serotonin. First, classifier models based on convolutional neural networks (CNN) are trained on sequence features to classify DNA ligands as either high response or low response to serotonin. Second, support vector machine (SVM) regression models are trained to predict relative optical response values for DNA sequences. Finally, we demonstrate with validation experiments that integrating the predictions of ensembles of the highest quality CNN classifiers and SVM regression models leads to the best predictions of both high and low response sequences. With our ML approaches, we discovered five new DNA-SWNT sensors with higher fluorescence intensity response to serotonin than obtained previously. Overall, the explored ML approaches introduce an important new tool to predict useful DNA sequences, which can be used for discovery of new DNA-based sensors and nanobiotechnologies.
SARS-CoV-2 hijacks p38β/MAPK11 to promote virus replication
Authors: Higgins Christina A. , Nilsson-Payant Benjamin E. , Kurland Andrew P. , Ye Chengjin , Yaron Tomer , Johnson Jared L. , Bonaventure Boris , Adhikary Prithy , Golynker Ilona , Panis Maryline , Danziger Oded , Rosenberg Brad R. , Cantley Lewis C. , Martinez-Sobrido Luis , tenOever Benjamin R. , Johnson Jeffrey R.
Published: August 2021

SARS-CoV-2, the causative agent of the COVID-19 pandemic, drastically modifies infected cells in an effort to optimize virus replication. Included is the activation of the host p38 mitogen-activated protein kinase (MAPK) pathway, which plays a major role in inflammation and is a central driver of COVID-19 clinical presentations. Inhibition of p38/MAPK activity in SARS-CoV-2-infected cells reduces both cytokine production and viral replication. Here, we combined genetic screening with quantitative phosphoproteomics to better understand interactions between the p38/MAPK pathway and SARS-CoV-2. We found that several components of the p38/MAPK pathway impacted SARS-CoV-2 replication and that p38β is a critical host factor for virus replication, and it prevents activation of the type-I interferon pathway. Quantitative phosphoproteomics uncovered several SARS-CoV-2 nucleocapsid phosphorylation sites near the N-terminus that were sensitive to p38 inhibition. Similar to p38β depletion, mutation of these nucleocapsid residues was associated with reduced virus replication and increased activation of type-I interferon signaling. Taken together, this study reveals a unique proviral function for p38β that is not shared with p38α and supports exploring p38β inhibitor development as a strategy towards developing a new class of COVID-19 therapies.

Importance

SARS-CoV-2 is the causative agent of the COVID-19 pandemic that has claimed millions of lives since its emergence in 2019. SARS-CoV-2 infection of human cells requires the activity of several cellular pathways for successful replication. One such pathway, the p38 mitogen-activated protein kinase (MAPK) pathway, is required for virus replication and disease pathogenesis. Here, we applied systems biology approaches to understand how MAPK pathways benefit SARS-CoV-2 replication to inform the development of novel COVID-19 drug therapies.
Cannabidiol activates neuronal Kv7 channels
Authors: Niday Zachary , Heckman Laurel , Jo Sooyeon , Zhang Han-Xiong Bear , Fujita Akie , Shim Jaehoon , Pandey Roshan , Jandal Hoor Al , Jayakar Selwyn , Smith Jennifer A. , Woolf Clifford J. , Bean Bruce P.
Published: August 2021

Cannabidiol (CBD), a chemical found in the Cannabis sativa plant, is a clinically effective antiepileptic drug whose mechanism of action is unknown. Using a fluorescence-based thallium flux assay, we performed a large-scale screen and found enhancement of flux through heterologously-expressed human Kv7.2/7.3 channels by CBD. Using patch clamp recordings, we found that CBD at low concentrations activates Kv7.2/7.3 channels at subthreshold voltages, with 100 nM CBD producing a doubling of current at -50 mV. CBD shifted the voltage-dependence of channels in the hyperpolarizing direction, producing a shift in the midpoint of activation by ∼-14 mV at 300 nM. CBD also effectively enhanced native M-current in both mouse superior cervical ganglion neurons and rat hippocampal neurons. The potent enhancement of Kv2/7.3 channels by CBD seems likely to contribute to its effectiveness as an antiepileptic drug by reducing neuronal hyperexcitability.
Accounting for the “transcendent self”: spirituality, narcissism, testimony and gift
Authors: Achilli Giulia , Busco Cristiano , Giovannoni Elena
Published: August 2021

Purpose

The paper explores the process of construction of the “accountable self”, particularly as this process engages with the spirituality of the self. This study examines the “space of accountability” within which the accountable self constructs itself as such and investigates how different accounts of the self are drawn upon in the making of this space, both defining and transcending it.

Design/methodology/approach

The paper relies upon archival material concerning accounting and accountability practices about the project for building the altar of St. Ignatius in the Church of Gesù, Rome, Italy (1691–1706). This study examines calculative and narrative accounts about the project from the perspective of the superintendent, who was the sole person accountable for the building works.

Findings

Whereas calculative accounts enabled the self to account for actions within the specific space of accountability of the project, narrative accounts opened up this space, providing for a testimony of actions and a gift of accountability towards future indefinite others. This process was prompted by the spirituality of the self and the narcissistic gratification of fulfilling this spirituality.

Originality/value

The paper adds to the literature on the accountable self and to theological perspectives into accountability. This study suggests exploring how different accounts of the self engage with each other through testimony, gift, narcissism and spirituality in the construction of the accountable self, providing for a “transcendent” space of accountability. This research also adds to studies on narrative accounts by showing that they are drawn upon alongside calculative accounts in the construction of the transcendent, accountable self.
What drives persuasion to choose healthy and ecological food at hotel buffets: message, receiver or sender?
Authors: Volgger Michael , Cozzio Claudia , Taplin Ross
Published: August 2021

Purpose

The effectiveness of a message to persuade tourists to consume healthier and more ecological food may be influenced by (1) the message content, (2) the message sender and (3) the receiver of the message. This study analyses effective persuasion of tourists by simultaneously investigating how these three characteristics influence tourists' healthy and ecological food choices at hotel buffets.

Design/methodology/approach

A randomised 4 × 2 between-subject experimental design, replicated in two hotels, collected perceptions of 329 participants on four persuasive messages aimed at increasing food consumption in a realistic and natural setting at hotel buffets. The eight treatments included four persuasive messages (placebo appeal, health appeal, environmental appeal, local origin appeal), each with and without endorsement (i.e. with/without a specific sender).

Findings

Message content, in particular health and local provenance-related messages, and the characteristics of the receiver (tourists' attitudes and habits) influence food choices on holiday while the sender (endorsement) was found to be less influential. This implies that appropriate messages can persuade tourists to eat in a considerate manner from hotel buffets, especially for tourists with favourable attitudes and everyday behaviours.

Originality/value

This paper contributes to theory and practice in persuasive communication to encourage healthier and more ecological choices in hedonistic consumption. Specifically, this paper is the first to present an integrated empirical analysis on the simultaneous influence of (1) message content, (2) presence of an identifiable sender and (3) receiver characteristics, on healthy and ecological eating behaviour of tourists.