Sandblasting promotes shrub encroachment in arid grasslands.

Shrub encroachment is a common ecological state transition in global drylands and has myriad adverse effects on grasslands and the services they provide. This physiognomic shift is often ascribed to changes in climate (e.g. precipitation) and disturbance regimes (e.g. grazing and fire), but this remains debated. Aeolian processes are known to impact resource distribution in drylands, but their potential role in grassland-to-shrubland state changes has received little attention. We quantified the effects of 'sandblasting' (abrasive damage by wind-blown soil) on the ecophysiology of dryland grass vs shrub functional types using a portable wind tunnel to test the hypothesis that grasses would be more susceptible to sandblasting than shrubs and, thus, reinforce transitions to shrub dominance in wind-erodible grasslands when climate- or disturbance-induced reductions in ground cover occur. Grasses and shrubs responded differently to sandblasting, wherein water-use efficiency declined substantially in grasses, but only slightly in shrubs, owing to grasses having greater increases in day/nighttime leaf conductance and transpiration. The differential ecophysiological response to sandblasting exhibited by grass and shrub functional types could consequently alter the vegetation dynamics in dryland grasslands in favour of the xerophytic shrubs. Sandblasting could thus be an overlooked driver of shrub encroachment in wind-erodible grasslands.

STARTRAC analyses of scRNAseq data from tumor models reveal T cell dynamics and therapeutic targets.

Single-cell RNA sequencing is a powerful tool to examine cellular heterogeneity, novel markers and target genes, and therapeutic mechanisms in human cancers and animal models. Here, we analyzed single-cell RNA sequencing data of T cells obtained from multiple mouse tumor models by PCA-based subclustering coupled with TCR tracking using the STARTRAC algorithm. This approach revealed various differentiated T cell subsets and activation states, and a correspondence of T cell subsets between human and mouse tumors. STARTRAC analyses demonstrated peripheral T cell subsets that were developmentally connected with tumor-infiltrating CD8+ cells, CD4+ Th1 cells, and T reg cells. In addition, large amounts of paired TCRα/ß sequences enabled us to identify a specific enrichment of paired public TCR clones in tumor. Finally, we identified CCR8 as a tumor-associated T reg cell marker that could preferentially deplete tumor-associated T reg cells. We showed that CCR8-depleting antibody treatment provided therapeutic benefit in CT26 tumors and synergized with anti-PD-1 treatment in MC38 and B16F10 tumor models.

Efficacy of antibiotic prophylaxis prior to tympanoplasty for contaminated cholesteatoma.

OBJECTIVES: To evaluate the efficacy of combined antistaphylococcal and antipseudomonal preoperative antibiotics for preventing surgical site infections following tympanoplasty and mastoidectomy with contaminated cholesteatoma. STUDY DESIGN: Retrospective chart review. METHODS: Medical records of patients who underwent tympanoplasty ± mastoidectomy for cholesteatoma were reviewed. Only cases considered to have contaminated or dirty surgical fields were included. The primary outcome measure was occurrence of postoperative surgical site infections, perichondritis, pinna abscess, periotic cellulitis, or periotic abscess requiring systemic antibiotic therapy or surgical intervention. RESULTS: The charts of 326 patients who underwent tympanoplasty ± mastoidectomy were reviewed. Of those, 195 met inclusion criteria. Preoperative antibiotics included clindamycin and ceftazidime or gentamicin. Patients treated with no perioperative antibiotics had a surgical site infection rate of 11%, and those treated with perioperative antibiotics had a rate of 1% (P = 0.02). CONCLUSION: Administration of preoperative antibiotics to cover staphylococcal and pseudomonal species may prevent surgical site infections with tympanoplasty ± mastoidectomy for contaminated cholesteatoma. LEVEL OF EVIDENCE: 4. Laryngoscope, 126:2363-2366, 2016.

Magnetic resonance imaging in a guinea pig model of inner ear decompression sickness and barotrauma.

OBJECTIVES/HYPOTHESIS: Scuba diving may cause severe hearing loss and vertigo due to inner ear barotrauma and decompression sickness. These may be difficult to differentiate clinically. Decompression sickness requires costly and potentially dangerous hyperbaric therapy, whereas such treatment may worsen barotrauma. The objective of this study was to assess the potential utility of magnetic resonance imaging to identify and distinguish blood from air in the inner ear, manifestations of barotrauma and decompression sickness, using a guinea pig model. STUDY DESIGN: Prospective animal trial. METHODS: Magnetic resonance of the head was performed at 3 Tesla, pre- and postinjection of 2, 4, or 10 µL of air or blood through the round window into the perilymph. With this model, 2 µL has been shown to cause hearing loss. Images were reviewed by a neuroradiologist blinded to the treatment. RESULTS: All 14 normal ears, five of seven blood- and five of seven air-injected ears, were correctly interpreted. Two blood- and one air-injected ear were interpreted as indeterminate. One air-injected ear was incorrectly interpreted as blood. CONCLUSIONS: Magnetic resonance reliably distinguishes small volumes of air and blood in the guinea pig inner ear. Magnetic resonance should be evaluated for its utility in the diagnosis of inner ear barotrauma and decompression sickness in scuba divers. LEVEL OF EVIDENCE: NA Laryngoscope, 126:2106-2109, 2016.

Structural biology. Structural basis for Notch1 engagement of Delta-like 4.

Notch receptors guide mammalian cell fate decisions by engaging the proteins Jagged and Delta-like (DLL). The 2.3 angstrom resolution crystal structure of the interacting regions of the Notch1-DLL4 complex reveals a two-site, antiparallel binding orientation assisted by Notch1 O-linked glycosylation. Notch1 epidermal growth factor-like repeats 11 and 12 interact with the DLL4 Delta/Serrate/Lag-2 (DSL) domain and module at the N-terminus of Notch ligands (MNNL) domains, respectively. Threonine and serine residues on Notch1 are functionalized with O-fucose and O-glucose, which act as surrogate amino acids by making specific, and essential, contacts to residues on DLL4. The elucidation of a direct chemical role for O-glycans in Notch1 ligand engagement demonstrates how, by relying on posttranslational modifications of their ligand binding sites, Notch proteins have linked their functional capacity to developmentally regulated biosynthetic pathways.

Exome sequencing of Bardet-Biedl syndrome patient identifies a null mutation in the BBSome subunit BBIP1 (BBS18).

BACKGROUND: Bardet-Biedl syndrome (BBS) is a recessive and genetically heterogeneous ciliopathy characterised by retinitis pigmentosa, obesity, kidney dysfunction, postaxial polydactyly, behavioural dysfunction and hypogonadism. 7 of the 17 BBS gene products identified to date assemble together with the protein BBIP1/BBIP10 into the BBSome, a protein complex that ferries signalling receptors to and from cilia. METHODS AND RESULTS: Exome sequencing performed on a sporadic BBS case revealed for the first time a homozygous stop mutation (NM_001195306: c.173T>G, p.Leu58*) in the BBIP1 gene. This mutation is pathogenic since no BBIP1 protein could be detected in fibroblasts from the patient, and BBIP1[Leu58*] is unable to associate with the BBSome subunit BBS4. CONCLUSIONS: These findings identify BBIP1 as the 18th BBS gene (BBS18) and suggest that BBSome assembly may represent a unifying pathomechanism for BBS.

Cilia grow by taking a bite out of the cell.

Autophagy and primary cilium assembly have long been known to be induced by the same conditions in cultured cells. Two recent studies in Nature-Tang et al. (2013) and Pampliega et al. (2013)-link the two processes, suggesting that a specialized autophagy pathway near the basal body regulates cilium assembly.

Cand1 promotes assembly of new SCF complexes through dynamic exchange of F box proteins.

The modular SCF (Skp1, cullin, and F box) ubiquitin ligases feature a large family of F box protein substrate receptors that enable recognition of diverse targets. However, how the repertoire of SCF complexes is sustained remains unclear. Real-time measurements of formation and disassembly indicate that SCF(Fbxw7) is extraordinarily stable, but, in the Nedd8-deconjugated state, the cullin-binding protein Cand1 augments its dissociation by one-million-fold. Binding and ubiquitylation assays show that Cand1 is a protein exchange factor that accelerates the rate at which Cul1-Rbx1 equilibrates with multiple F box protein-Skp1 modules. Depletion of Cand1 from cells impedes recruitment of new F box proteins to pre-existing Cul1 and profoundly alters the cellular landscape of SCF complexes. We suggest that catalyzed protein exchange may be a general feature of dynamic macromolecular machines and propose a hypothesis for how substrates, Nedd8, and Cand1 collaborate to regulate the cellular repertoire of SCF complexes.

Endolymphatic hydrops perspectives 2012.

PURPOSE OF REVIEW: Endolymphatic hydrops remains a significant cause of morbidity secondary to vertigo, hearing loss, and tinnitus. The purpose of this report is to summarize the most clinically relevant publications on endolymphatic hydrops over the past 2 years. RECENT FINDINGS: Hydrops has historically been a diagnosis of exclusion, but recent efforts has shown a role for MRI with intratympanic gadolinium. Cochrane reviews of intratympanic dexamethasone and gentamicin found inadequate level 1 evidence to support their use. SUMMARY: High-level evidence to guide therapy is lacking. MRI holds potential for definitive diagnosis.

Chemical genetics screen for enhancers of rapamycin identifies a specific inhibitor of an SCF family E3 ubiquitin ligase.

The target of rapamycin (TOR) plays a central role in eukaryotic cell growth control. With prevalent hyperactivation of the mammalian TOR (mTOR) pathway in human cancers, strategies to enhance TOR pathway inhibition are needed. We used a yeast-based screen to identify small-molecule enhancers of rapamycin (SMERs) and discovered an inhibitor (SMER3) of the Skp1-Cullin-F-box (SCF)(Met30) ubiquitin ligase, a member of the SCF E3-ligase family, which regulates diverse cellular processes including transcription, cell-cycle control and immune response. We show here that SMER3 inhibits SCF(Met30) in vivo and in vitro, but not the closely related SCF(Cdc4). Furthermore, we demonstrate that SMER3 diminishes binding of the F-box subunit Met30 to the SCF core complex in vivo and show evidence for SMER3 directly binding to Met30. Our results show that there is no fundamental barrier to obtaining specific inhibitors to modulate function of individual SCF complexes.

Detection of sequential polyubiquitylation on a millisecond timescale.

The pathway by which ubiquitin chains are generated on substrate through a cascade of enzymes consisting of an E1, E2 and E3 remains unclear. Multiple distinct models involving chain assembly on E2 or substrate have been proposed. However, the speed and complexity of the reaction have precluded direct experimental tests to distinguish between potential pathways. Here we introduce new theoretical and experimental methodologies to address both limitations. A quantitative framework based on product distribution predicts that the really interesting new gene (RING) E3 enzymes SCF(Cdc4) and SCF(beta-TrCP) work with the E2 Cdc34 to build polyubiquitin chains on substrates by sequential transfers of single ubiquitins. Measurements with millisecond time resolution directly demonstrate that substrate polyubiquitylation proceeds sequentially. Our results present an unprecedented glimpse into the mechanism of RING ubiquitin ligases and illuminate the quantitative parameters that underlie the rate and pattern of ubiquitin chain assembly.