Dynamic conformational changes of a tardigrade group-3 late embryogenesis abundant protein modulate membrane biophysical properties

A number of intrinsically disordered proteins (IDPs) encoded in stress-tolerant organisms, such as tardigrade, can confer fitness advantage and abiotic stress tolerance when heterologously expressed. Tardigrade-specific disordered proteins including the cytosolic-abundant heat-soluble proteins are proposed to confer stress tolerance through vitrification or gelation, whereas evolutionarily conserved IDPs in tardigrades may contribute to stress tolerance through other biophysical mechanisms. In this study, we characterized the mechanism of action of an evolutionarily conserved, tardigrade IDP, HeLEA1, which belongs to the group-3 late embryogenesis abundant (LEA) protein family. HeLEA1 homologs are found across different kingdoms of life. HeLEA1 is intrinsically disordered in solution but shows a propensity for helical structure across its entire sequence. HeLEA1 interacts with negatively charged membranes via dynamic disorder-to-helical transition, mainly driven by electrostatic interactions. Membrane interaction of HeLEA1 is shown to ameliorate excess surface tension and lipid packing defects. HeLEA1 localizes to the mitochondrial matrix when expressed in yeast and interacts with model membranes mimicking inner mitochondrial membrane. Yeast expressing HeLEA1 shows enhanced tolerance to hyperosmotic stress under nonfermentative growth and increased mitochondrial membrane potential. Evolutionary analysis suggests that although HeLEA1 homologs have diverged their sequences to localize to different subcellular organelles, all homologs maintain a weak hydrophobic moment that is characteristic of weak and reversible membrane interaction. We suggest that such dynamic and weak protein-membrane interaction buffering alterations in lipid packing could be a conserved strategy for regulating membrane properties and represent a general biophysical solution for stress tolerance across the domains of life.

Dysphagia Outcomes Following Surgical Management of Unilateral Vocal Fold Immobility: A Systematic Review and Meta-analysis

OBJECTIVE

To assess dysphagia outcomes following surgical management of unilateral vocal fold immobility (UVFI) in adults.

DATA SOURCES

Ovid MEDLINE, Embase, Web of Science, and Cochrane Central.

REVIEW METHODS

A structured literature search was utilized, and a 2-researcher systematic review was performed following PRISMA guidelines. Extractable data were pooled, and a quantitative analysis was performed with a random effects model to analyze treatment outcome and complications by procedure.

RESULTS

A total of 416 publications were screened and 26 met inclusion criteria. Subjects encompassed 959 patients with UVFI who underwent 916 procedures (n = 547, injection laryngoplasty; n = 357, laryngeal framework surgery; n = 12, laryngeal reinnervation). An overall 615 were identified as having dysphagia as a result of UVFI and had individually extractable outcome data, which served as the basis for a quantitative meta-analysis. In general, dysphagia outcomes after all medialization procedures were strongly positive. Quantitative analysis demonstrated a success rate estimate of 90% (95% CI, 75%-100%) for injection laryngoplasty and 92% (95% CI, 87%-97%) for laryngeal framework surgery. The estimated complication rate was 7% (95% CI, 2%-13%) for injection laryngoplasty and 15% (95% CI, 10%-20%) for laryngeal framework surgery, with minor complications predominating. Although laryngeal reinnervation could not be assessed quantitatively due to low numbers, qualitative analysis demonstrated consistent benefit for a majority of patients for each procedure.

CONCLUSION

Dysphagia due to UVFI can be improved in a majority of patients with surgical procedures intended to improve glottal competence, with a low risk of complications. Injection laryngoplasty and laryngeal framework surgery appear to be efficacious and safe, and laryngeal reinnervation may be a promising new option for select patients.

Medical and social determinants of health as predictors of adverse outcomes in patients with inflammatory bowel disease

There is a growing recognition that social determinants of health (SDOH) influence outcomes in patients with chronic diseases. This study aimed to investigate the influence of SDOH on outcomes in patients with inflammatory bowel disease (IBD). We conducted a retrospective cohort study of adult patients with IBD from 1996 to 2019. Patients were identified using ICD-10 codes for ulcerative colitis and Crohn's disease, and chart review was performed to validate the diagnosis and extract clinical information. SDOH factors including food security, financial resources, and transportation were self-reported by the patient. Random forest models were trained and tested in R to predict either IBD-related hospitalization or surgery. A total of 175 patients were studied, and the majority reported no financial resource, food security, or transportation concerns. For the model using clinical predictors, the sensitivity was 0.68 and specificity was 0.77 with an area under the receiver operating characteristic curve (AUROC) of 0.77. The model's performance did not significantly improve with the addition of SDOH information (AUROC of 0.78); however, model performance did vary by phenotype (AUROC of 0.86 for patients with Crohn's disease and AUROC of 0.68 for patients with ulcerative colitis). Further research is needed to understand the role of SDOH factors and IBD-related outcomes.

Interactions between mobile genetic elements: An anti-phage gene in an integrative and conjugative element protects host cells from predation by a temperate bacteriophage

Most bacterial genomes contain horizontally acquired and transmissible mobile genetic elements, including temperate bacteriophages and integrative and conjugative elements. Little is known about how these elements interact and co-evolved as parts of their host genomes. In many cases, it is not known what advantages, if any, these elements provide to their bacterial hosts. Most strains of Bacillus subtilis contain the temperate phage SPß and the integrative and conjugative element ICEBs1. Here we show that the presence of ICEBs1 in cells protects populations of B. subtilis from predation by SPß, likely providing selective pressure for the maintenance of ICEBs1 in B. subtilis. A single gene in ICEBs1 (yddK, now called spbK for SPß killing) was both necessary and sufficient for this protection. spbK inhibited production of SPß, during both activation of a lysogen and following de novo infection. We found that expression spbK, together with the SPß gene yonE constitutes an abortive infection system that leads to cell death. spbK encodes a TIR (Toll-interleukin-1 receptor)-domain protein with similarity to some plant antiviral proteins and animal innate immune signaling proteins. We postulate that many uncharacterized cargo genes in ICEs may confer selective advantage to cells by protecting against other mobile elements.

Chromosomes from virtually all organisms contain genes that were horizontally acquired. In bacteria, many of the horizontally acquired genes are located in mobile genetic elements, elements that promote their own transfer from one cell to another. These elements include viruses and conjugative elements that are parts of the host genome and they can contain genes involved in metabolism, pathogenesis, symbiosis, and antibiotic resistances. Interactions between these elements are poorly understood. Furthermore, the majority of these elements confer no obvious benefit to host cells. We found that the presence of an integrative and conjugative element (ICE) in a bacterial genome protects host cells from predation by a bacteriophage (virus). There is a single gene in the integrative and conjugative element that confers this protection, and one gene in the bacteriophage that likely works together with the ICE gene. When expressed at the same time, these two genes cause cell death, before functional viruses can be made and released to kill other cells. We postulate that other ICEs may confer selective advantage to their host cells by protecting against other mobile elements.

Molecular mechanisms underlying the role of the centriolar CEP164-TTBK2 complex in ciliopathies

Cilia formation is essential for human life. One of the earliest events in the ciliogenesis program is the recruitment of tau-tubulin kinase 2 (TTBK2) by the centriole distal appendage component CEP164. Due to the lack of high-resolution structural information on this complex, it is unclear how it is affected in human ciliopathies such as nephronophthisis. Furthermore, it is poorly understood if binding to CEP164 influences TTBK2 activities. Here, we present a detailed biochemical, structural, and functional analysis of the CEP164-TTBK2 complex and demonstrate how it is compromised by two ciliopathic mutations in CEP164. Moreover, we also provide insights into how binding to CEP164 is coordinated with TTBK2 activities. Together, our data deepen our understanding of a crucial step in cilia formation and will inform future studies aimed at restoring CEP164 functionality in a debilitating human ciliopathy.

In vivo evidence for the cellular basis of central hypoventilation of Rett syndrome and pharmacological correction in the rat model

Rett syndrome (RTT) is a neurodevelopmental disorder caused mostly by mutations in the MECP2 gene. RTT patients show periodical hypoventilation attacks. The breathing disorder contributing to the high incidence of sudden death is thought to be due to depressed central inspiratory (I) activity via unknown cellular processes. Demonstration of such processes may lead to targets for pharmacological control of the RTT-type hypoventilation. We performed in vivo recordings from medullary respiratory neurons on the RTT rat model. To our surprise, both I and expiratory (E) neurons in the ventral respiratory column (VRC) increased their firing activity in Mecp2-null rats with severe hypoventilation. These I neurons including E-I phase-spanning and other I neurons remained active during apneas. Consistent with enhanced central I drive, ectopic phrenic discharges during expiration as well as apnea were observed in the Mecp2-null rats. Considering the increased I neuronal firing and ectopic phrenic activity, the RTT-type hypoventilation does not seem to be caused by depression in central I activity, neither reduced medullary I premotor output. This as well as excessive E neuronal firing as shown in our previous studies suggests inadequate synaptic inhibition for phase transition. We found that the abnormal respiratory neuronal firing, ectopic phrenic discharge as well as RTT-type hypoventilation all can be corrected by enhancing GABAergic inhibition. More strikingly, Mecp2-null rats reaching humane endpoints with severe hypoventilation can be rescued by GABAergic augmentation. Thus, defective GABAergic inhibition among respiratory neurons is likely to play a role in the RTT-type hypoventilation, which can be effectively controlled with pharmacological agents.

State of the Science in Tracheal Stents: A Scoping Review

OBJECTIVE

Recent material science advancements are driving tracheal stent innovation. We sought to assess the state of the science regarding materials and preclinical/clinical outcomes for tracheal stents in adults with benign tracheal disease.

METHODS

A comprehensive literature search in April 2021 identified 556 articles related to tracheal stents. One-hundred and twenty-eight full-text articles were reviewed and 58 were included in the final analysis. Datapoints examined were stent materials, clinical applications and outcomes, and preclinical findings, including emerging technologies.

RESULTS

In the 58 included studies, stent materials were metals (n = 28), polymers (n = 19), coated stents (n = 19), and drug-eluting (n = 5). Metals included nitinol, steel, magnesium alloys, and elgiloy. Studies utilized 10 different polymers, the most popular included polydioxanone, poly-l-lactic acid, poly(d,l-lactide-co-glycolide), and polycaprolactone. Coated stents employed a metal or polymer framework and were coated with polyurethane, silicone, polytetrafluoroethylene, or polyester, with some polymer coatings designed specifically for drug elution. Drug-eluting stents utilized mitomycin C, arsenic trioxide, paclitaxel, rapamycin, and doxycycline. Of the 58 studies, 18 were human and 40 were animal studies (leporine = 21, canine = 9, swine = 4, rat = 3, ovine/feline/murine = 1). Noted complications included granulation tissue and/or stenosis, stent migration, death, infection, and fragmentation.

CONCLUSION

An increasing diversity of materials and coatings are employed for tracheal stents, growing more pronounced over the past decade. Though most studies are still preclinical, awareness of tracheal stent developments is important in contextualizing novel stent concepts and clinical trials. Laryngoscope, 2021.

Two ABC transport systems carry out peptide uptake in Enterococcus faecalis: Their roles in growth and in uptake of sex pheromones

Enterococcal pheromone-inducible plasmids encode a predicted OppA-family secreted lipoprotein. In the case of plasmid pCF10, the protein is PrgZ, which enhances the mating response to cCF10 pheromone. OppA proteins generally function with associated OppBCDF ABC transporters to import peptides. In this study, we analyzed the potential interactions of PrgZ with two host-encoded Opp transporters using two pheromone-inducible fluorescent reporter constructs. Based on our results, we propose renaming these loci opp1 (OG1RF_10634-10639) and opp2 (OG1RF_12366-12370). We also examined the ability of the Opp1 and Opp2 systems to mediate import in the absence of PrgZ. Cells expressing PrgZ were able to import pheromone if either opp1 or opp2 was functional, but not if both opp loci were disrupted. In the absence of PrgZ, pheromone import was dependent on a functional opp2 system, including opp2A. Comparative structural analysis of the peptide-binding pockets of PrgZ, Opp1A, Opp2A, and the related Lactococcus lactis OppA protein, suggested that the robust pheromone-binding ability of PrgZ relates to a nearly optimal fit of the hydrophobic peptide, whereas binding ability of Opp2A likely results from a more open, promiscuous peptide-binding pocket similar to L. lactis OppA.

Background concentrations of Argon-39 in shallow soil gas

While radioisotopes of noble gases are known to be indicators of underground nuclear explosions (UNE), McIntyre et al. (2017) was the first to report the presence of ³⁹Ar in shallow soil gas in association with a decades old UNE. While this finding hinted at the potential application of ³⁹Ar to be used as an indicator of a UNE, doing so would also require an understanding of the natural concentrations of ³⁹Ar present in soil gas. Without knowing the expected range and variability of naturally occurring concentrations of ³⁹Ar, it is difficult to determine what measured concentrations would be indicative of an elevated concentration. This paper presents results from 16 soil gas samples and three atmospheric air samples collected from various locations across the western United States. Shallow soil gas samples were collected into self-contained underwater breathing apparatus (SCUBA) tanks using a custom-built soil gas sampling system and then processed and analyzed for ³⁹Ar. The measured concentrations of ³⁹Ar varied from atmospheric air concentrations to about 3.5 times atmospheric air concentrations (58 mBq/m³). The results presented here represent the first measurements of natural background ³⁹Ar concentrations in shallow soil gas. This data will be necessary if ³⁹Ar is to be used as an indicator of UNE.

Target-induced clustering activates Trim-Away of pathogens and proteins

Trim-Away is a recently developed technology that exploits off-the-shelf antibodies and the RING E3 ligase and cytosolic antibody receptor TRIM21 to carry out rapid protein depletion. How TRIM21 is catalytically activated upon target engagement, either during its normal immune function or when repurposed for targeted protein degradation, is unknown. Here we show that a mechanism of target-induced clustering triggers intermolecular dimerization of the RING domain to switch on the ubiquitination activity of TRIM21 and induce virus neutralization or drive Trim-Away. We harness this mechanism for selective degradation of disease-causing huntingtin protein containing long polyglutamine tracts and expand the Trim-Away toolbox with highly active TRIM21-nanobody chimeras that can also be controlled optogenetically. This work provides a mechanism for cellular activation of TRIM RING ligases and has implications for targeted protein degradation technologies.

Isothermal Titration Calorimetry

Calorimetry is a classical biophysical method that by definition measures heat. In isothermal titration calorimetry (ITC), the heat is the result of titrating interacting components together and allows direct determination of the thermodynamics for this process. The measured heat reflects the enthalpy change (ΔH), and the prospect of determining this in biological systems where high-resolution structural information is available has led to the possibility of rational thermodynamics-guided design of ligands. Although there are limitations to this approach due to the participation of solvent in the thermodynamics, ITC has become an established technique in many labs providing a valuable tool with which to quantify protein-protein interactions. With careful use, ITC can also provide additional insights into the binding process or be used in increasingly complex systems and where interaction is coupled to other molecular events.

Dual synaptic inhibitions of brainstem neurons by GABA and glycine with impact on Rett syndrome

Rett syndrome (RTT) is a neurodevelopmental disease caused mostly by mutations in the MECP2 gene. People with RTT show breathing dysfunction attributable to the high rate of sudden death. Previous studies have shown that insufficient GABA synaptic inhibition contributes to the breathing abnormalities in mouse models of RTT, while it remains elusive how the glycine system is affected. We found that optogenetic stimulation of GAD-expressing neurons in mice produced GABAergic and glycinergic postsynaptic inhibitions of neurons in the hypoglossal nucleus (XII) and the dorsal motor nucleus of vagus (DMNV). By sequential applications of bicuculline and strychnine, such inhibition appeared approximately 44% GABA_A ergic and 52% glycinergic in XII neurons, and approximately 49% GABA_A ergic and 46% glycinergic in DMNV neurons. Miniature inhibitory postsynaptic potentials (mIPSCs) in these neurons were approximately 47% GABA_A ergic and 49% glycinergic in XII neurons, and approximately 48% versus 50% in DMNV neurons, respectively. Consistent with the data, our single-cell polymerase chain reaction studies indicated that transcripts of GABA_A receptor γ2 subunit (GABA_A Rγ2) and glycine receptor β subunit (GlyRβ) were simultaneously expressed in these cells. In MeCP2^R168X mice, proportions of GABA_A ergic and glycinergic mIPSCs became approximately 28% versus 69% in XII neurons, and approximately 31% versus 66% in DMNV cells. In comparison with control mice, the GABA_A ergic and glycinergic mIPSCs decreased significantly in the XII and DMNV neurons from the MeCP2^R168X mice, so did the transcripts of GABA_A Rγ2 and GlyRβ. These results suggest that XII and DMNV neurons adopt dual GABA_A ergic and glycinergic synaptic inhibitions, and with Mecp2 disruption these neurons rely more on glycinergic synaptic inhibition.

Effect of structural stability on endolysosomal degradation and T-cell reactivity of major shrimp allergen tropomyosin

BACKGROUND

Tropomyosins are highly conserved proteins, an attribute that forms the molecular basis for their IgE antibody cross-reactivity. Despite sequence similarities, their allergenicity varies greatly between ingested and inhaled invertebrate sources. In this study, we investigated the relationship between the structural stability of different tropomyosins, their endolysosomal degradation patterns, and T-cell reactivity.

METHODS

We investigated the differences between four tropomyosins-the major shrimp allergen Pen m 1 and the minor allergens Der p 10 (dust mite), Bla g 7 (cockroach), and Ani s 3 (fish parasite)-in terms of IgE binding, structural stability, endolysosomal degradation and subsequent peptide generation, and T-cell cross-reactivity in a BALB/c murine model.

RESULTS

Tropomyosins displayed different melting temperatures, which did not correlate with amino acid sequence similarities. Endolysosomal degradation experiments demonstrated differential proteolytic digestion, as a function of thermal stability, generating different peptide repertoires. Pen m 1 (Tm 42°C) and Der p 10 (Tm 44°C) elicited similar patterns of endolysosomal degradation, but not Bla g 7 (Tm 63°C) or Ani s 3 (Tm 33°C). Pen m 1-specific T-cell clones, with specificity for regions highly conserved in all four tropomyosins, proliferated weakly to Der p 10, but did not proliferate to Bla g 7 and Ani s 3, indicating lack of T-cell epitope cross-reactivity.

CONCLUSIONS

Tropomyosin T-cell cross-reactivity, unlike IgE cross-reactivity, is dependent on structural stability rather than amino acid sequence similarity. These findings contribute to our understanding of cross-sensitization among different invertebrates and design of suitable T-cell peptide-based immunotherapies for shrimp and related allergies.

The antitussive cloperastine improves breathing abnormalities in a Rett Syndrome mouse model by blocking presynaptic GIRK channels and enhancing GABA release

Rett Syndrome (RTT) is an X-linked neurodevelopmental disorder caused mainly by mutations in the MECP2 gene. One of the major RTT features is breathing dysfunction characterized by periodic hypo- and hyperventilation. The breathing disorders are associated with increased brainstem neuronal excitability, which can be alleviated with GABA agonists. Since neuronal hypoexcitability occurs in the forebrain of RTT models, it is necessary to find pharmacological agents with a relative preference to brainstem neurons. Here we show evidence for the improvement of breathing disorders of Mecp2-disrupted mice with the brainstem-acting drug cloperastine (CPS) and its likely neuronal targets. CPS is an over-the-counter cough medicine that has an inhibitory effect on brainstem neuronal networks. In Mecp2-disrupted mice, CPS (30 mg/kg, i.p.) decreased the occurrence of apneas/h and breath frequency variation. GIRK currents expressed in HEK cells were inhibited by CPS with IC₅₀ 1 μM. Whole-cell patch clamp recordings in locus coeruleus (LC) and dorsal tegmental nucleus (DTN) neurons revealed an overall inhibitory effect of CPS (10 μM) on neuronal firing activity. Such an effect was reversed by the GABA_A receptor antagonist bicuculline (20 μM). Voltage clamp studies showed that CPS increased GABAergic sIPSCs in LC cells, which was blocked by the GABA_B receptor antagonist phaclofen. Functional GABAergic connections of DTN neurons with LC cells were shown. These results suggest that CPS improves breathing dysfunction in Mecp2-null mice by blocking GIRK channels in synaptic terminals and enhancing GABA release.

Membrane characteristics tune activities of endosomal and autophagic human VPS34 complexes

The lipid kinase VPS34 orchestrates diverse processes, including autophagy, endocytic sorting, phagocytosis, anabolic responses and cell division. VPS34 forms various complexes that help adapt it to specific pathways, with complexes I and II being the most prominent ones. We found that physicochemical properties of membranes strongly modulate VPS34 activity. Greater unsaturation of both substrate and non-substrate lipids, negative charge and curvature activate VPS34 complexes, adapting them to their cellular compartments. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) of complexes I and II on membranes elucidated structural determinants that enable them to bind membranes. Among these are the Barkor/ATG14L autophagosome targeting sequence (BATS), which makes autophagy-specific complex I more active than the endocytic complex II, and the Beclin1 BARA domain. Interestingly, even though Beclin1 BARA is common to both complexes, its membrane-interacting loops are critical for complex II, but have only a minor role for complex I.

Dynamic catch-bonding generates the large stall forces of cytoplasmic dynein

Cytoplasmic dynein is an important molecular motor involved in the transport of vesicular and macromolecular cargo along microtubules in cells, often in conjunction with kinesin motors. Dynein is larger and more complex than kinesin and the mechanism and regulation of its movement is currently the subject of intense research. While it was believed for a long time that dynein motors are relatively weak in terms of the force they can generate, recent studies have shown that interactions with regulatory proteins confer large stall forces comparable to those of kinesin. This paper reports on a theoretical study which suggests that these large stall forces may be the result of an emergent, ATP-dependent, bistability resulting in a dynamic catch-bonding behavior that can cause the motor to switch between high and low load-force states.

CCDC61/VFL3 Is a Paralog of SAS6 and Promotes Ciliary Functions

Centrioles are cylindrical assemblies whose peripheral microtubule array displays a 9-fold rotational symmetry that is established by the scaffolding protein SAS6. Centriole symmetry can be broken by centriole-associated structures, such as the striated fibers in Chlamydomonas that are important for ciliary function. The conserved protein CCDC61/VFL3 is involved in this process, but its exact role is unclear. Here, we show that CCDC61 is a paralog of SAS6. Crystal structures of CCDC61 demonstrate that it contains two homodimerization interfaces that are similar to those found in SAS6, but result in the formation of linear filaments rather than rings. Furthermore, we show that CCDC61 binds microtubules and that residues involved in CCDC61 microtubule binding are important for ciliary function in Chlamydomonas. Together, our findings suggest that CCDC61 and SAS6 functionally diverged from a common ancestor while retaining the ability to scaffold the assembly of basal body-associated structures or centrioles, respectively.

Signalling lymphocyte activation molecule family member 9 is found on select subsets of antigen-presenting cells and promotes resistance to Salmonella infection

Signalling lymphocyte activation molecule family member 9 (SLAMF9) is an orphan receptor of the CD2/SLAM family of leucocyte surface proteins. Examination of SLAMF9 expression and function indicates that SLAMF9 promotes inflammation by specialized subsets of antigen‐presenting cells. Within healthy liver and circulating mouse peripheral blood mononuclear cells, SLAMF9 is expressed on CD11b⁺, Ly6C⁻, CD11c^low, F4/80^low, MHC‐II⁺, CX₃CR1⁺ mononuclear phagocytes as well as plasmacytoid dendritic cells. In addition, SLAMF9 can be found on peritoneal B1 cells and small (F4/80^low), but not large (F4/80^high), peritoneal macrophages. Upon systemic challenge with Salmonella enterica Typhimurium, Slamf9^−/− mice were impaired in their ability to clear the infection from the liver. In humans, SLAMF9 is up‐regulated upon differentiation of monocytes into macrophages, and lipopolysaccharide stimulation of PMA‐differentiated, SLAMF9 knockdown THP‐1 cells showed an essential role of SLAMF9 in production of granulocyte–macrophage colony‐stimulating factor, tumour necrosis factor‐α, and interleukin‐1β. Taken together, these data implicate SLAMF9 in the initiation of inflammation and clearance of bacterial infection.

Methionine in a protein hydrophobic core drives tight interactions required for assembly of spider silk

Web spiders connect silk proteins, so-called spidroins, into fibers of extraordinary toughness. The spidroin N-terminal domain (NTD) plays a pivotal role in this process: it polymerizes spidroins through a complex mechanism of dimerization. Here we analyze sequences of spidroin NTDs and find an unusually high content of the amino acid methionine. We simultaneously mutate all methionines present in the hydrophobic core of a spidroin NTD from a nursery web spider’s dragline silk to leucine. The mutated NTD is strongly stabilized and folds at the theoretical speed limit. The structure of the mutant is preserved, yet its ability to dimerize is substantially impaired. We find that side chains of core methionines serve to mobilize the fold, which can thereby access various conformations and adapt the association interface for tight binding. Methionine in a hydrophobic core equips a protein with the capacity to dynamically change shape and thus to optimize its function.

Spider silk is of interest in material science research. Here the authors show that the tight binding of a spider silk protein domain relies on the amino acid methionine, which is abundant in the domain core where it facilitates dynamic shape adaption of the binding interface.

Maneuvering Clinical Pathways for Ulcerative Colitis

PURPOSE OF REVIEW

Recent years have brought about several advances in the treatment of patients with ulcerative colitis (UC). Here, we discuss salient recommendations of recent treatment guidelines; review the efficacy, safety, and real-world data of vedolizumab and tofacitinib; appraise their place vis-à-vis established agents; and consider the newly proposed approaches of risk-stratified and treat-to-target therapy.

RECENT FINDINGS

Once daily oral mesalamine dosing is equivalent to split dosing in mild-moderate UC. Real-world data are accumulating on the effectiveness and safety of vedolizumab for moderate to severe UC, while there are few such data on the most recently approved agent, tofacitinib. High-dose infliximab is being investigated for severe UC. New approaches are challenging the established paradigm of selecting therapy based on current disease activity. The risk-stratified approach incorporates long-term risk as well as the current burden of inflammation. The treat-to-target approach aims at improved long-term outcomes by adjusting therapy to resolve intestinal inflammation. The therapeutic options for UC are continually expanding. Risk-stratified therapy and the treat-to-target approach represent paradigm shifts in UC management. Optimal disease control requires an individualized approach that takes into consideration current inflammatory burden, long-term risk, patient preferences, and ongoing assessment of response to treatment.

Hexameric assembly of the AAA+ protein McrB is necessary for GTPase activity

McrBC is one of the three modification-dependent restriction enzymes encoded by the Escherichia coli K12 chromosome. Amongst restriction enzymes, McrBC and its close homologues are unique in employing the AAA+ domain for GTP hydrolysis-dependent activation of DNA cleavage. The GTPase activity of McrB is stimulated by the endonuclease subunit McrC. It had been reported previously that McrB and McrC subunits oligomerise together into a high molecular weight species. Here we conclusively demonstrate using size exclusion chromatography coupled multi-angle light scattering (SEC-MALS) and images obtained by electron cryomicroscopy that McrB exists as a hexamer in solution. Furthermore, based on SEC-MALS and SAXS analyses of McrBC and the structure of McrB, we propose that McrBC is a complex of two McrB hexamers bridged by two subunits of McrC, and that the complete assembly of this complex is integral to its enzymatic activity. We show that the nucleotide-dependent oligomerisation of McrB precedes GTP hydrolysis. Mutational studies show that, unlike other AAA+ proteins, the catalytic Walker B aspartate is required for oligomerisation.

Structural insights into the critical DNA damage sensors DNA-PKcs, ATM and ATR

ATM, ATR and DNA-PKCs are key effectors of DNA Damage response and have been extensively linked to tumourigenesis and survival of cancer cells after radio/chemotherapy. Despite numerous efforts, the structures of these proteins remained elusive until very recently. The resolution revolution in Cryo-EM allowed for molecular details of these proteins to be seen for the first time. Here we provide a comprehensive review of the structures of ATM, ATR and DNA-PKcs and their complexes and expand with observations springing from our own cryo-EM studies. These observations include a novel conformation of ATR and novel dimeric arrangements of DNA-PKcs.

Three-dimensional damage morphologies of thermomechanically deformed sintered nanosilver die attachments for power electronics modules

A time-lapse study of thermomechanical fatigue damage has been undertaken using three-dimensional X-ray computer tomography. Morphologies were extracted from tomography data and integrated with data from microscopy modalities at different resolution levels. This enables contextualization of some of the fine-scale properties which underpin the large-scale damage observed via tomography. Lateral views of crack development are presented, which show networks analogous to mud-cracks. Crack fronts which develop in the most porous regions within the sintered attachment layer travel across the boundary into the copper substrate. The propagation characteristics of these cracks within the substrate are analysed. Evidence is provided of heterogeneous densification within the sintered joint under power cycling, and this is shown to play a major role in driving the initiation and propagation of the cracks. Examination of the texture (differing levels of X-ray absorption) of virtual cross-sectional images reveals the origins of the nonuniformity of densification. Finally, cracks within the sintered joint are shown to have a negligible impact on the conduction pathway of the joint due to their aspect ratio and orientation with respect to the assembly. LAY DESCRIPTION: This paper concerns the use of three-dimensional (3D) X-ray tomography, a nondestructive technique, to perform cradle-to-grave studies of sintered nanosilver die-attachments under operation. Sintered nanosilver die-attachments have been proposed as a more reliable and environmentally friendly alternative to solder alloy joints for emerging power electronics module designs. However, their degradation mechanisms are not as well understood. This same sample-study is about observing how the fine-scale structure of a sintered attachment evolves and degrades over time. Using 3D tomography affords otherwise infeasible perspectives, such as virtual cross-sections in the lateral plane of the attachment. These perspectives provide qualitative information which elucidates the degradation mechanisms. They demonstrate, for example, that the structure of the sintered attachment densifies under operation, and a consequence of this is the formation of shrinkage cracks in the most porous regions, much like mud-cracks. Other imaging techniques (metallographic etching and scanning electron microscopy) have been used in correlation with 3D renderings of these cracks to analyse their propagation and reveal their relationship both with the internal structure of the sintered attachment itself, and the structure of the substrate to which it is joined. It is shown that the cracks develop within the sintered attachment layer and eventually cross over into the substrate. A comparison of two sintered attachments with contrasting bulk porosities allows the effect of initial bond quality on crack development to be examined.

Mecp2 Disruption in Rats Causes Reshaping in Firing Activity and Patterns of Brainstem Respiratory Neurons

People with Rett Syndrome (RTT), a neurodevelopmental disorder caused by mutations in the MECP2 gene, have breathing abnormalities manifested as periodical hypoventilation with compensatory hyperventilation, which are attributable to a high incidence of sudden death. Similar breathing abnormalities have been found in animal models with Mecp2 disruptions. Although RTT-type hypoventilation is believed to be due to depressed central inspiratory activity, whether this is true remains unknown. Here we show evidence for reshaping in firing activity and patterns of medullary respiratory neurons in RTT-type hypoventilation without evident depression in inspiratory neuronal activity. Experiments were performed in decerebrate rats in vivo. In Mecp2-null rats, abnormalities in breathing patterns were apparent in both decerebrate rats and awake animals, suggesting that RTT-type breathing abnormalities take place in the brainstem without forebrain input. In comparison to their wild-type counterparts, both inspiratory and expiratory neurons in Mecp2-null rats extended their firing duration, and fired more action potentials during each burst. No changes in inspiratory or expiratory neuronal distributions were found. Most inspiratory neurons started firing in the middle of expiration and changed their firing pattern to a phase-spanning type. The proportion of post-inspiratory neurons was reduced in the Mecp2-null rats. With the increased firing activity of both inspiratory and expiratory neurons in null rats, phrenic discharges shifted to a slow and deep breathing pattern. Thus, the RTT-type hypoventilation appears to result from reshaping of firing activity of both inspiratory and expiratory neurons without evident depression in central inspiratory activity.

pH-Driven RNA Strand Separation under Prebiotically Plausible Conditions

Replication of nucleic acids in the absence of genetically encoded enzymes represents a critical process for the emergence of cellular life. Repeated separation of complementary RNA strands is required to achieve multiple cycles of chemical replication, yet thermal denaturation under plausible prebiotic conditions is impaired by the high temperatures required to separate long RNA strands and by concurrent degradation pathways, the latter accelerated by divalent metal ions. Here we show how the melting temperature of oligoribonucleotide duplexes can be tuned by changes in pH, enabling the separation of RNA strands at moderate temperatures. At the same time, the risk of phosphodiester bond cleavage is reduced under the acid denaturation conditions herein described, both in the presence and in the absence of divalent metal ions. Through a combination of ultraviolet and circular dichroism thermal studies and gel electrophoresis, we demonstrate the relevance of geological pH oscillations in the context of the RNA strand separation problem. Our results reveal new insights in the field of prebiotic chemistry, supporting plausible geochemical scenarios in which non-enzymatic RNA replication might have taken place.

Update on the Use of Thiopurines and Methotrexate in Inflammatory Bowel Disease

PURPOSE OF REVIEW

The increased use of biologic agents over the past two decades has led to a reappraisal of the role of the immunomodulators (thiopurines and methotrexate) in the treatment of inflammatory bowel disease. The purpose of this review is to summarize recent data on the use of thiopurines and methotrexate either as monotherapy or as part of combination therapy with biologic agents.

RECENT FINDINGS

Recent studies have addressed the need for concomitant immunomodulatory therapy in treatment-naïve patients starting anti-TNF-α therapy, the appropriate dose of the immunomodulator in this setting, the minimum duration of combination therapy, and the possible mechanisms by which immunomodulators enhance the effectiveness of anti-TNF-α agents. Little is known about the role of immunomodulators in combination with agents belonging to other classes of biologic therapies. Recent studies have shown that methotrexate is not effective in inducing or maintaining remission in ulcerative colitis. Finally, several studies have broadened our understanding of the infection and malignancy risks of the immunomodulators. Immunomodulators continue to have a place in the treatment of inflammatory bowel disease. However, with the ever-increasing list of biologic agents, properly positioning the immunomodulators within the overall therapeutic scheme is a complicated task. In order to optimize outcomes, each patient requires an individualized approach, which takes into account risks, benefits, cost, alternatives, and patient preferences.

RNA-directed activation of cytoplasmic dynein-1 in reconstituted transport RNPs

Polarised mRNA transport is a prevalent mechanism for spatial control of protein synthesis. However, the composition of transported ribonucleoprotein particles (RNPs) and the regulation of their movement are poorly understood. We have reconstituted microtubule minus end-directed transport of mRNAs using purified components. A Bicaudal-D (BicD) adaptor protein and the RNA-binding protein Egalitarian (Egl) are sufficient for long-distance mRNA transport by the dynein motor and its accessory complex dynactin, thus defining a minimal transport-competent RNP. Unexpectedly, the RNA is required for robust activation of dynein motility. We show that a cis-acting RNA localisation signal promotes the interaction of Egl with BicD, which licenses the latter protein to recruit dynein and dynactin. Our data support a model for BicD activation based on RNA-induced occupancy of two Egl-binding sites on the BicD dimer. Scaffolding of adaptor protein assemblies by cargoes is an attractive mechanism for regulating intracellular transport.

In our cells, tiny molecular motors transport the components necessary for life’s biological processes from one location to another. They do so by loading their cargo, and burning up chemical fuel to carry it along pathways made of filaments. For example, one such motor, called dynein, can move molecules of messenger RNA (mRNA) to specific locations within the cell. There, the mRNA will be used as a template to create proteins, which will operate at exactly the right place.

Transporting mRNA in this way is critical in processes such as embryonic development and the formation of memories; yet, this mechanism is still poorly understood. Previous work suggested that the mRNA is simply a passenger of the dynein motor, but McClintock et al. asked if this is really the case. Instead, could mRNA regulate its own sorting by controlling the activity of dynein?

Studying mRNA trafficking within the complex molecular environment of a cell is challenging, so mRNA transporting machinery was recreated in the laboratory. Only the proteins necessary to build a working system were included in the experiments. In addition to the filaments, the components included dynein and a complex of proteins known as dynactin, which allows the motor to move together with a protein called BICD2. A protein named Egalitarian was used to link the mRNA to BICD2.

By filming fluorescently labelled proteins and mRNAs, McClintock et al. discovered that mRNA strongly promotes the movement of the dynein motor. A structured section in the mRNA acts as a docking area for two copies of Egalitarian. This activates BICD2, which then binds to dynein and dynactin, thereby completing the transport machinery. According to these results, the mRNA directs the assembly of the system that will carry it within the cell.

Viruses such as HIV and herpesvirus hijack dynein motors to have their genetic information moved around a cell in order to propagate infection. Understanding precisely how mRNA is transported may help to develop new strategies to fight these viruses.

Expression of myxovirus-resistance protein A: a possible marker of muscle disease activity and autoantibody specificities in juvenile dermatomyositis

Aims

To evaluate the relationship between expression of myxovirus‐resistance protein A (MxA) protein on muscle biopsies by immunohistochemistry and disease activity in juvenile dermatomyositis (JDM) patients. Also, another aim was to investigate whether the expression of MxA is related with myositis‐specific autoantibodies (MSA) status in JDM patients.

Methods

103 patients (median aged 6.3, interquartile range 0.5–15.9) enrolled in the Juvenile Dermatomyositis Cohort and Biomarker Study (JDCBS). Muscle biopsies were stained with MxA and scored. Clinical data at initial presentation were collected and autoantibodies were analysed. Multiple linear regression analysis was performed to estimate the association between MxA expression on muscle fibres and muscle disease activity, and MSA status.

Results

Expression of MxA protein on JDM samples was identified in 61.2%. There was a significant association between MxA scores and Childhood Myositis Assessment Scale (CMAS) (P = 0.002), and Manual Muscle Testing of Eight Muscles (MMT8) (P = 0.026). CMAS and MMT8 scores were significantly lower in the group of patients with strong MxA expression. MxA scores differed according to MSA subgroups (P = 0.002). Patients with positive nuclear matrix protein 2 autoantibodies had strong MxA expression, whereas anti‐melanoma differentiation‐associated gene 5 positive patients had no or weak MxA expression.

Conclusions

This study reveals the significant association between level of MxA expression on muscle fibres and clinical measures of muscular disease activity in JDM patients and MSA status. This confirms type I interferonopathies in muscle fibres of JDM patients which could help with improving treatment outcome in JDM patients and underscoring the distinct pathophysiological pathways in different MSA status.

Epithelioid Granulomas Associate With Increased Severity and Progression of Crohn's Disease, Based on 6-Year Follow-Up

BACKGROUND & AIMS

Epithelioid granulomas are characteristics of a subset of patients with Crohn's disease (CD), but their significance, with regard to disease progression and severity, is unclear. We investigated the relationship between granulomas and CD severity over a 6-year time period in a large cohort of patients.

METHODS

We performed a retrospective study of patients with CD seen at the Inflammatory Bowel Disease Center at the University of Pittsburgh; data were collected from 2009 through 2014 and patients were assigned to groups with and without histologic evidence of granuloma. Demographic, clinical (including disease activity, quality of life, medication use, and healthcare utilization), and laboratory data were used in association and survival analyses. Differences between groups were evaluated using the Mann-Whitney U-test for continuous variables.

RESULTS

Of 1466 patients with CD, granulomas were identified in 187 (12.8%). In the subset of patients who underwent surgery, 21.0% had granulomas. The presence of granuloma was associated with increased serum levels of c-reactive protein (odds ratio [OR], 2.9; 95% CI, 2.078-4.208; P < .0001), younger mean age at diagnosis (23.6 ± 11.3 years in patients with granulomas vs 27.9 ± 13.3 years in patients without; P = .0005), higher rates of stricturing or penetrating disease phenotype, higher rates of steroid and narcotic use, and higher healthcare utilization. Among patients that underwent surgery, the presence of granulomas was associated with need for repeat surgery during the 6-year observation period (OR, 2.5; 95% CI, 1.54-4.02; P = .0002). Infliximab use was associated with detection of granuloma in a significantly lower proportion of surgical specimens compared to patients who had not been treated with a biologic agent (OR, 0.22; 95 CI, 0.05-0.97; P = .03).

CONCLUSIONS

Epithelioid granulomas develop in less than 13% of patients with CD, and are associated with a more aggressive disease phenotype. Patients who have undergone surgery for CD and have granulomas are at increased risk for repeat surgery within 6 years.

Disease-Associated Mutations in CEP120 Destabilize the Protein and Impair Ciliogenesis

Ciliopathies are a group of genetic disorders caused by a failure to form functional cilia. Due to a lack of structural information, it is currently poorly understood how ciliopathic mutations affect protein functionality to give rise to the underlying disease. Using X-ray crystallography, we show that the ciliopathy-associated centriolar protein CEP120 contains three C2 domains. The point mutations V194A and A199P, which cause Joubert syndrome (JS) and Jeune asphyxiating thoracic dystrophy (JATD), respectively, both reduce the thermostability of the second C2 domain by targeting residues that point toward its hydrophobic core. Genome-engineered cells homozygous for these mutations have largely normal centriole numbers but show reduced CEP120 levels, compromised recruitment of distal centriole markers, and deficient cilia formation. Our results provide insight into the disease mechanism of two ciliopathic mutations in CEP120, identify putative binding partners of CEP120 C2B, and suggest a complex genotype-phenotype relation of the CEP120 ciliopathy alleles.

Direct binding of CEP85 to STIL ensures robust PLK4 activation and efficient centriole assembly

Centrosomes are required for faithful chromosome segregation during mitosis. They are composed of a centriole pair that recruits and organizes the microtubule-nucleating pericentriolar material. Centriole duplication is tightly controlled in vivo and aberrations in this process are associated with several human diseases, including cancer and microcephaly. Although factors essential for centriole assembly, such as STIL and PLK4, have been identified, the underlying molecular mechanisms that drive this process are incompletely understood. Combining protein proximity mapping with high-resolution structural methods, we identify CEP85 as a centriole duplication factor that directly interacts with STIL through a highly conserved interaction interface involving a previously uncharacterised domain of STIL. Structure-guided mutational analyses in vivo demonstrate that this interaction is essential for efficient centriolar targeting of STIL, PLK4 activation and faithful daughter centriole assembly. Taken together, our results illuminate a molecular mechanism underpinning the spatiotemporal regulation of the early stages of centriole duplication.

Intracellular antibody signalling is regulated by phosphorylation of the Fc receptor TRIM21

Cell surface Fc receptors activate inflammation and are tightly controlled to prevent autoimmunity. Antibodies also simulate potent immune signalling from inside the cell via the cytosolic antibody receptor TRIM21, but how this is regulated is unknown. Here we show that TRIM21 signalling is constitutively repressed by its B-Box domain and activated by phosphorylation. The B-Box occupies an E2 binding site on the catalytic RING domain by mimicking E2-E3 interactions, inhibiting TRIM21 ubiquitination and preventing immune activation. TRIM21 is derepressed by IKKβ and TBK1 phosphorylation of an LxxIS motif in the RING domain, at the interface with the B-Box. Incorporation of phosphoserine or a phosphomimetic within this motif relieves B-Box inhibition, promoting E2 binding, RING catalysis, NF-κB activation and cytokine transcription upon infection with DNA or RNA viruses. These data explain how intracellular antibody signalling is regulated and reveal that the B-Box is a critical regulator of RING E3 ligase activity.

Antibodies are molecules made by the immune system that protect us from infections. They were discovered over 100 years ago, and for most of that time scientists thought they only worked in the bloodstream. Yet recent research showed that when a virus infects our cells it also carries antibodies in with it. Once inside the cell, a protein called TRIM21 recognises the antibody-covered virus and – together with other proteins called ubiquitin enzymes – targets it for destruction via the cell’s waste disposal system. At the same time TRIM21 sends a signal to the cell’s nucleus to activate certain genes that protect cells across the body from subsequent infection.

The genes activated by TRIM21 have potent antiviral activity. Yet they can also damage the body’s own tissues if they are switched on at the wrong time, which may lead to autoimmune diseases like rheumatoid arthritis and multiple sclerosis. It is thus critical that TRIM21 is carefully regulated and only activated during an infection, but it was not clear how this is achieved.

Dickson, Fletcher et al. now show that although TRIM21 is made all the time and is always ready to detect an incoming virus it is made in an inactive state. This is because part of TRIM21, called a B-Box, inhibits the protein’s own activity. This was an unexpected discovery because, although the B-Box domain is found in around 100 other human proteins, it was unclear what it did. Dickson, Fletcher et al. then combined structural biology and biochemical approaches to show that the B-Box mimics specific enzymes that work with TRIM21, and blocks them from binding to it. This keeps TRIM21 in an inactive state.

Next, Dickson, Fletcher et al. discovered that TRIM21 becomes active when a chemical tag, specifically a phosphate group, is added to the protein. This modification displaces the B-Box, allowing ubiquitin enzymes to bind to TRIM21 and switch on its activity. Further experiments then showed that this process helps regulate TRIM21 during infections with different viruses, including rhinovirus – the virus behind the common cold – and adenovirus – a common cause of respiratory infection.

Antibodies are now used to treat many medical conditions, but present technologies are based on our understanding of how antibodies work outside cells. By revealing the basis of antibody immunity inside cells, these new findings may lead to new treatments for a range of conditions. Future studies could also explore how failures in the TRIM21 system contribute to autoimmune diseases.

Observed parent-child feeding dynamics in relation to child body mass index and adiposity

BACKGROUND

Restrictive feeding is associated with child overweight; however, the majority of studies used parent-report questionnaires.

OBJECTIVES

The relationship between child adiposity measures and directly observed parent and child behaviours were tested using a novel behavioural coding system (BCS).

METHODS

Data from 109 children, participants in a twin study and their mothers, were analyzed. Parent-child dyads were video-recorded twice in the laboratory, while children ate ad libitum from a buffet lunch. Mother and child behaviours were assessed using the BCS. Height, body weight and body fat were directly measured for each child. Associations between child adiposity measures and average BCS behaviour (i.e. pooled across visits) were tested using partial correlations adjusting for child age.

RESULTS

Regarding discouragement prompts, child body mass index (BMI) z-score was significantly associated with a greater rate of total discouragements (per minute, min^-1 ), nonverbal discouragements (min^-1 ) and temporary (delay) discouragements (min^-1 ) (p < 0.05). Child percent body fat was associated with greater nonverbal discouragements (min^-1 ). Regarding encouragement prompts, child BMI z-score was significantly associated with a greater rate of total encouragements (min^-1 ), nonverbal encouragements (min^-1 ) and reward encouragements (min^-1 ). Child BMI z-score and percent body fat were both positively associated with greater maternal health encouragements (min^-1 ). Associations with encouragement to eat prompts were no longer significant when accounting for the dependence among twins (being part of the same family).

CONCLUSIONS

Heavier children received greater maternal discouragements to eat and, with qualifications, encouragements to eat. The role of nonverbal parenting cues warrants further research regarding child eating regulation and obesity.

Effect of Chromoendoscopy Filters on Visualization of KTP Laser-Associated Tissue Changes: A Cadaveric Animal Model

Standard KTP laser (potassium titanyl phosphate) wavelength-specific protective eyewear often impairs visualization of tissue changes during laser treatment. This sometimes necessitates eyewear removal to evaluate tissue effects, which wastes time and poses safety concerns. The objective was to determine if "virtual" or "electronic" chromoendoscopy filters, as found on some endoscopy platforms, could alleviate the restricted visualization inherent to protective eyewear. A KTP laser was applied to porcine laryngeal tissue and recorded via video laryngoscopy with 1 optical (Olympus Narrow Band Imaging) and 8 digital (Pentax Medical I-scan) chromoendoscopy filters. Videos were viewed by 11 otolaryngologists wearing protective eyewear. Using a discrete visual analog scale, they rated each filter on its ability to improve visualization,. No filter impaired visualization; 5 of 9 improved visualization. Based on statistical significance, the number of positive responses, and the lack of negative responses, narrow band imaging and the I-scan tone enhancement filter for leukoplakia performed best. These filters could shorten procedure time and improve safety; therefore, further clinical evaluation is warranted.

Mutualism between co-occurring plant species in South Africa's Mediterranean climate heathland is mediated by birds

Interactions among plant species via pollinators vary from competitive to mutualistic and can influence the probability of stable coexistence of plant species. We aimed to determine the nature of the interaction via flower visitors between Leucospermum conocarpodendron and Mimetes fimbriifolius, two shrubs in the Proteaceae that share many ecological traits and coexist on the Cape Peninsula, South Africa. To assess the extent of pollinator sharing we analysed nectar properties and recorded the pollinator fauna, their behaviour and contribution to seed set. To test for competition via interspecific pollen transfer, we recorded the movement patterns of pollinators and quantified pollen loads. To determine the effect of co-flowering on visitation rates we recorded visits in stands that varied in the density of the two species. We found that the species produce similar rewards and share pollinating Cape Sugarbirds (Promerops cafer). Interspecific pollen transfer is avoided by placing pollen on different parts of the bird. Both species are visited by nectar-thieving Orange-breasted Sunbirds (Anthobaphes violacea). Insects and autonomous self-pollination contributed little to seed set. Pollinator visits increased with conspecific density in both species, and the slope of the increase was steepest in the presence of high densities of the co-occurring plant species. Nectar thief visits also increased with conspecific density in both species, but the slope declined with increasing density of the co-occurring species. Co-occurrence enhanced pollinator visits and alleviated nectar robbing in both plant species, consistent with mutualisms. Mutualism within a trophic level is unusual, but may help to explain the stable coexistence of ecologically similar species.

Exploration of Protein Unfolding by Modelling Calorimetry Data from Reheating

Studies of protein unfolding mechanisms are critical for understanding protein functions inside cells, de novo protein design as well as defining the role of protein misfolding in neurodegenerative disorders. Calorimetry has proven indispensable in this regard for recording full energetic profiles of protein unfolding and permitting data fitting based on unfolding pathway models. While both kinetic and thermodynamic protein stability are analysed by varying scan rates and reheating, the latter is rarely used in curve-fitting, leading to a significant loss of information from experiments. To extract this information, we propose fitting both first and second scans simultaneously. Four most common single-peak transition models are considered: (i) fully reversible, (ii) fully irreversible, (iii) partially reversible transitions, and (iv) general three-state models. The method is validated using calorimetry data for chicken egg lysozyme, mutated Protein A, three wild-types of haloalkane dehalogenases, and a mutant stabilized by protein engineering. We show that modelling of reheating increases the precision of determination of unfolding mechanisms, free energies, temperatures, and heat capacity differences. Moreover, this modelling indicates whether alternative refolding pathways might occur upon cooling. The Matlab-based data fitting software tool and its user guide are provided as a supplement.

Effects of early-life exposure to THIP on brainstem neuronal excitability in the Mecp2-null mouse model of Rett syndrome before and after drug withdrawal

Rett syndrome (RTT) is mostly caused by mutations of the X‐linked MECP2 gene. Although the causal neuronal mechanisms are still unclear, accumulating experimental evidence obtained from Mecp2^−/Y mice suggests that imbalanced excitation/inhibition in central neurons plays a major role. Several approaches may help to rebalance the excitation/inhibition, including agonists of GABA_A receptors (GABA_AR). Indeed, our previous studies have shown that early‐life exposure of Mecp2‐null mice to the extrasynaptic GABA_AR agonist THIP alleviates several RTT‐like symptoms including breathing disorders, motor dysfunction, social behaviors, and lifespan. However, how the chronic THIP affects the Mecp2^−/Y mice at the cellular level remains elusive. Here, we show that the THIP exposure in early lives markedly alleviated hyperexcitability of two types of brainstem neurons in Mecp2^−/Y mice. In neurons of the locus coeruleus (LC), known to be involved in breathing regulation, the hyperexcitability showed clear age‐dependence, which was associated with age‐dependent deterioration of the RTT‐like breathing irregularities. Both the neuronal hyperexcitability and the breathing disorders were relieved with early THIP treatment. In neurons of the mesencephalic trigeminal nucleus (Me5), both the neuronal hyperexcitability and the changes in intrinsic membrane properties were alleviated with the THIP treatment in Mecp2‐null mice. The effects of THIP on both LC and Me5 neuronal excitability remained 1 week after withdrawal. Persistent alleviation of breathing abnormalities in Mecp2^−/Y mice was also observed a week after THIP withdrawal. These results suggest that early‐life exposure to THIP, a potential therapeutic medicine, appears capable of controlling neuronal hyperexcitability in Mecp2^−/Y mice, which occurs in the absence of THIP in the recording solution, lasts at least 1 week after withdrawal, and may contribute to the RTT‐like symptom mitigation.

Kymograph analysis with high temporal resolution reveals new features of neurofilament transport kinetics

We have used kymograph analysis combined with edge detection and an automated computational algorithm to analyze the axonal transport kinetics of neurofilament polymers in cultured neurons at 30 ms temporal resolution. We generated 301 kymographs from 136 movies and analyzed 726 filaments ranging from 0.6 to 42 µm in length, representing ∼37,000 distinct moving and pausing events. We found that the movement is even more intermittent than previously reported and that the filaments undergo frequent, often transient, reversals which suggest that they can engage simultaneously with both anterograde and retrograde motors. Average anterograde and retrograde bout velocities (0.9 and 1.2 µm s^-1 , respectively) were faster than previously reported, with maximum sustained bout velocities of up to 6.6 and 7.8 µm s^-1 , respectively. Average run lengths (∼1.1 µm) and run times (∼1.4 s) were in the range reported for molecular motor processivity in vitro, suggesting that the runs could represent the individual processive bouts of the neurofilament motors. Notably, we found no decrease in run velocity, run length or run time with increasing filament length, which suggests that either the drag on the moving filaments is negligible or that longer filaments recruit more motors.

Oncoidal granular iron formation in the Mesoarchaean Pongola Supergroup, southern Africa: Textural and geochemical evidence for biological activity during iron deposition

We document the discovery of the first granular iron formation (GIF) of Archaean age and present textural and geochemical results that suggest these formed through microbial iron oxidation. The GIF occurs in the Nconga Formation of the ca. 3.0-2.8 Ga Pongola Supergroup in South Africa and Swaziland. It is interbedded with oxide and silicate facies micritic iron formation (MIF). There is a strong textural control on iron mineralization in the GIF not observed in the associated MIF. The GIF is marked by oncoids with chert cores surrounded by magnetite and calcite rims. These rims show laminated domal textures, similar in appearance to microstromatolites. The GIF is enriched in silica and depleted in Fe relative to the interbedded MIF. Very low Al and trace element contents in the GIF indicate that chemically precipitated chert was reworked above wave base into granules in an environment devoid of siliciclastic input. Microbially mediated iron precipitation resulted in the formation of irregular, domal rims around the chert granules. During storm surges, oncoids were transported and deposited in deeper water environments. Textural features, along with positive δ⁵⁶ Fe values in magnetite, suggest that iron precipitation occurred through incomplete oxidation of hydrothermal Fe²⁺ by iron-oxidizing bacteria. The initial Fe³⁺ -oxyhydroxide precipitates were then post-depositionally transformed to magnetite. Comparison of the Fe isotope compositions of the oncoidal GIF with those reported for the interbedded deeper water iron formation (IF) illustrates that the Fe²⁺ pathways and sources for these units were distinct. It is suggested that the deeper water IF was deposited from the evolved margin of a buoyant Fe²⁺_aq -rich hydrothermal plume distal to its source. In contrast, oncolitic magnetite rims of chert granules were sourced from ambient Fe²⁺_aq -depleted shallow ocean water beyond the plume.

Outcomes of laryngohyoid suspension techniques in an ovine model of profound oropharyngeal dysphagia

OBJECTIVES/HYPOTHESIS

To evaluate the efficacy of various techniques of laryngohyoid suspension in the elimination of aspiration utilizing a cadaveric ovine model of profound oropharyngeal dysphagia.

STUDY DESIGN

Animal study.

METHODS

The head and neck of a Dorper cross ewe was placed in the lateral fluoroscopic view. Five conditions were tested: baseline, thyroid cartilage to hyoid approximation (THA), thyroid cartilage to hyoid to mandible (laryngohyoid) suspension (LHS), LHS with cricopharyngeus muscle myotomy (LHS-CPM), and cricopharyngeus muscle myotomy (CPM) alone. Five 20-mL trials of barium sulfate were delivered into the oropharynx under fluoroscopy for each condition. Outcome measures included the penetration aspiration scale (PAS) and the National Institutes of Health (NIH) Swallow Safety Scale (NIH-SSS).

RESULTS

Median baseline PAS and NIH-SSS scores were 8 and 6, respectively, indicating severe impairment. THA scores were not improved from baseline. LHS alone reduced the PAS to 1 (P = .025) and NIH-SSS to 2 (P = .025) from baseline. LHS-CPM reduced the PAS to 1 (P = .025) and NIH-SSS to 0 (P = .025) from baseline. CPM alone did not improve scores. LHS-CPM displayed improved NIH-SSS over LHS alone (P = .003).

CONCLUSIONS

This cadaveric model represents end-stage profound oropharyngeal dysphagia such as what could result from severe neurological insult. CPM alone failed to improve fluoroscopic outcomes in this model. Thyrohyoid approximation also failed to improve outcomes. LHS significantly improved both PAS and NIH-SSS. The addition of CPM to LHS resulted in improvement over suspension alone.

LEVEL OF EVIDENCE

NA. Laryngoscope, 127:E422-E427, 2017.

The feasibility of gamma radiation sterilization for decellularized tracheal grafts

OBJECTIVES/HYPOTHESIS

The most promising stem cell-derived tracheal transplantation approach is dependent upon the use of decellularized tracheal grafts. It has been assumed that a sterilization step, such as gamma radiation, would damage the delicate extracellular matrix of the graft, thus rendering it less viable for cellular repopulation, although this has not been thoroughly investigated.

STUDY DESIGN

Laboratory-based comparative analysis.

METHODS

Fifteen murine tracheas of strain C57/B-6 mice were obtained. Thirteen were subjected to a detergent-enzymatic decellularization process. Of these decellularized tracheas (DT), eight were irradiated, exposing five tracheas to a radiation level of 25 kGy (DT25) and three to 5 kGy (DT5). Two were left untreated. The two untreated tracheas, two DTs, and two DT25s were prepared and examined using both scanning and transmission electron microscopy. Bioburden calculations were obtained from three DTs, three DT25s, and three DT5s by homogenization, serial dilution, and streak plating.

RESULTS

Electron microscopy of untreated fresh tracheas and DTs showed a slight qualitative degradation of cartilage ultrastructure due to the decellularization process. In contrast, examination of DT25 shows significant degradation including poor overall preservation of cartilage architecture with disorganized collagen fibers. The nonirradiated DTs had a calculated bacterial bioburden of 7.8 × 10⁷ to 3.4 × 10⁸ colony-forming units per gram. Both the DT25 and DT5 specimens were found to have a bioburden of zero.

CONCLUSIONS

Gamma radiation at 25 kGy degrades the architecture of decellularized tracheal grafts. These ultrastructural changes may prove detrimental to graft viability; however, bioburden calculations suggest that a 5 kGy radiation dose may be sufficient for sterilization.

LEVEL OF EVIDENCE

NA Laryngoscope, 127:E258-E264, 2017.

Structures of closed and open conformations of dimeric human ATM

ATM (ataxia-telangiectasia mutated) is a phosphatidylinositol 3-kinase-related protein kinase (PIKK) best known for its role in DNA damage response. ATM also functions in oxidative stress response, insulin signaling, and neurogenesis. Our electron cryomicroscopy (cryo-EM) suggests that human ATM is in a dynamic equilibrium between closed and open dimers. In the closed state, the PIKK regulatory domain blocks the peptide substrate-binding site, suggesting that this conformation may represent an inactive or basally active enzyme. The active site is held in this closed conformation by interaction with a long helical hairpin in the TRD3 (tetratricopeptide repeats domain 3) domain of the symmetry-related molecule. The open dimer has two protomers with only a limited contact interface, and it lacks the intermolecular interactions that block the peptide-binding site in the closed dimer. This suggests that the open conformation may be more active. The ATM structure shows the detailed topology of the regulator-interacting N-terminal helical solenoid. The ATM conformational dynamics shown by the structures represent an important step in understanding the enzyme regulation.

Effect of Intravenous or Perivascular Injection of Synthetic Adrenocorticotropic Hormone on Stimulation Test Results in Dogs

Background

Standard protocols for adrenocorticotropic hormone (ACTH) stimulation testing (ACTHst) often involve intravenous (IV) injection of corticotropin. ACTH might be unintentionally injected into the perivascular (PV) space.

Objective

To compare stimulation test results after IV and PV injections of ACTH.

Animals

Twenty privately owned dogs were studied: 10 healthy and 10 with trilostane‐treated naturally occurring hyperadrenocorticism (HAC).

Methods

Prospective study. Each of 20 dogs underwent 2 ACTHst not <4 nor more than 14 days apart. Five healthy and 5 HAC dogs had an IV ACTHst first and PV second; 5 healthy and 5 HAC dogs had a PV ACTHst first and IV second. Blood samples for measurement of serum cortisol concentration were collected before and 1 hour after ACTH administration.

Results

No significant difference in results was demonstrated when comparing serum cortisol concentrations after IV and PV ACTH administration in all 20 dogs (median μg/dL; interval μg/dL: 8.2; 1.4–17.4 versus 7.8; 0.9–16.9; P = .23). No significant difference in results was demonstrated when comparing serum cortisol concentrations after IV and PV ACTH administration in the 10 healthy dogs (median μg/dL; interval μg/dL: 10.9; 7.3–17.4 versus 10.6; 7.1–16.9; P = .54) or in the 10 HAC dogs (median μg/dL; interval μg/dL: 6.3; 1.4–8.6 versus 5.2; 0.9–8.7; P = .061).

Conclusions and Clinical Importance

Perivascular administration of ACTH does not significantly alter stimulation test results in healthy dogs or in dogs with HAC undergoing therapy with trilostane.

The Ciliopathy-Associated Cep104 Protein Interacts with Tubulin and Nek1 Kinase

Cilia are thin cell projections with essential roles in cell motility, fluid movement, sensing, and signaling. They are templated from centrioles that dock against the plasma membrane and subsequently extend their peripheral microtubule array. The molecular mechanisms underpinning cilia assembly are incompletely understood. Cep104 is a key factor involved in cilia formation and length regulation that rides on the ends of elongating and shrinking cilia. It is mutated in Joubert syndrome, a genetically heterogeneous ciliopathy. Here we provide structural and biochemical data that Cep104 contains a tubulin-binding TOG (tumor overexpressed gene) domain and a novel C2HC zinc finger array. Furthermore, we identify the kinase Nek1, another ciliopathy-associated protein, as a potential binding partner of this array. Finally, we show that Nek1 competes for binding to Cep104 with the distal centriole-capping protein CP110. Our data suggest a model for Cep104 activity during ciliogenesis and provide a novel link between Cep104 and Nek1.