Mucus carbohydrate composition correlates with scleractinian coral phylogeny.

The mucus surface layer serves vital functions for scleractinian corals and consists mainly of carbohydrates. Its carbohydrate composition has been suggested to be influenced by environmental conditions (e.g., temperature, nutrients) and microbial pressures (e.g., microbial degradation, microbial coral symbionts), yet to what extend the coral mucus composition is determined by phylogeny remains to be tested. To investigate the variation of mucus carbohydrate compositions among coral species, we analyzed the composition of mucosal carbohydrate building blocks (i.e., monosaccharides) for five species of scleractinian corals, supplemented with previously reported data, to discern overall patterns using cluster analysis. Monosaccharide composition from a total of 23 species (belonging to 14 genera and 11 families) revealed significant differences between two phylogenetic clades that diverged early in the evolutionary history of scleractinian corals (i.e., complex and robust; p = 0.001, R2 = 0.20), mainly driven by the absence of arabinose in the robust clade. Despite considerable differences in environmental conditions and sample analysis protocols applied, coral phylogeny significantly correlated with monosaccharide composition (Mantel test: p < 0.001, R2 = 0.70). These results suggest that coral mucus carbohydrates display phylogenetic dependence and support their essential role in the functioning of corals.

Adding Vertebral Bone Quality to the Fusion Risk Score: Does It Improve Predictions of Postoperative Complications?

STUDY DESIGN: Retrospective review of prospectively collected data. OBJECTIVE: The current study evaluates whether the addition of the Vertebral Bone Quality (VBQ) score to the Fusion Risk Score (FRS) improves its ability to predict perioperative outcomes. SUMMARY OF BACKGROUND DATA: The FRS was developed to assess preoperative risk in patients undergoing thoracic and lumbar fusions. It includes patient-derived and surgical variables, but it does not include one that directly accounts for bone health. The VBQ score allows assessment of bone quality and has been shown to correlate to DEXA-measured bone mineral density (BMD) scores. METHODS: The VBQ score was weighted based on a regression model and then added to the FRS (FRS/VBQ). The ability of the two scores to predict the outcomes was then assessed using the area under the curve (AUC). PATIENT SAMPLE: Patients undergoing elective thoracic and lumbar spinal fusion from January 2019 to June 2020 were included. OUTCOME MEASURES: The study evaluated various perioperative adverse outcomes, including major and minor adverse events, discharge other than home, extended length of stay, 90-day emergency department visits, 90-day readmission, and 90-day and 2-year reoperation rates. RESULTS: A total of 353 met the inclusion and exclusion criteria. The FRS/VBQ demonstrated improved predictive ability compared with the FRS alone when evaluating 90-day reoperation. Both scores showed fair predictive ability for any adverse event, major adverse events, minor adverse events, and 2-year reoperation rates, with AUCs ranging from 0.700 to 0.737. Both had poor predictive ability for the other outcomes. CONCLUSIONS: Adding VBQ to the FRS significantly enhances its predictive accuracy for reoperation rate. This updated risk score provides a more comprehensive understanding of a patient's preoperative risk profile, aiding both patients and physicians in assessing surgical risks and optimizing outcomes through preoperative risk stratification. LEVEL OF EVIDENCE: 3.

Optimized Solid-Phase Mesh-Enhanced Sorption from Headspace (SPMESH) for Rapid Sub-ng/kg Measurements of 3-Isobutyl-2-methoxypyrazine (IBMP) in Grapes.

Parallel extraction of headspace volatiles from multiwell plates using sorbent sheets (HS-SPMESH) followed by direct analysis in real-time high-resolution mass spectrometry (DART-HRMS) can be used as a rapid alternative to solid-phase micro-extraction (SPME) gas-chromatography mass-spectrometry (GC-MS) for trace level volatile analyses. However, an earlier validation study of SPMESH-DART-MS using 3-isobutyl-2-methoxypyrazine (IBMP) in grape juice showed poor correlation between SPMESH-DART-MS and a gold standard SPME-GC-MS around the compound's odor detection threshold (<10 ng/kg) in grape juice, and lacked sufficient sensitivity to detect IBMP at this concentration in grape homogenate. In this work, we report on the development and validation of an improved SPMESH extraction approach that lowers the limit of detection (LOD < 0.5 ng/kg), and regulates crosstalk between wells (<0.5%) over a calibration range of 0.5−100 ng/kg. The optimized SPMESH-DART-MS method was validated using Cabernet Sauvignon and Merlot grape samples harvested from commercial vineyards in the central valley of California (n = 302) and achieved good correlation and agreement with SPME-GC-MS (R2 = 0.84) over the native range of IBMP (<0.5−20 ng/kg). Coupling of SPMESH to a lower resolution triple quadrupole (QqQ)-MS via a new JumpShot-HTS DART source also achieved low ng/kg detection limits, and throughput was improved through positioning stage optimizations which reduced time spent on intra-well SPMESH areas.

Nocturnal dissolved organic matter release by turf algae and its role in the microbialization of reefs.

The increased release of dissolved organic matter (DOM) by algae has been associated with the fast but inefficient growth of opportunistic microbial pathogens and the ongoing degradation of coral reefs. Turf algae (consortia of microalgae and macroalgae commonly including cyanobacteria) dominate benthic communities on many reefs worldwide. Opposite to other reef algae that predominantly release DOM during the day, turf algae containing cyanobacteria may additionally release large amounts of DOM at night. However, this night-DOM release and its potential contribution to the microbialization of reefs remains to be investigated.We first tested the occurrence of hypoxic conditions at the turf algae-water interface, as a lack of oxygen will facilitate the production and release of fermentation intermediates as night-time DOM. Second, the dissolved organic carbon (DOC) release by turf algae was quantified during day time and nighttime, and the quality of day and night exudates as food for bacterioplankton was tested. Finally, DOC release rates of turf algae were combined with estimates of DOC release based on benthic community composition in 1973 and 2013 to explore how changes in benthic community composition affected the contribution of night-DOC to the reef-wide DOC production.A rapid shift from supersaturated to hypoxic conditions at the turf algae-water interface occurred immediately after the onset of darkness, resulting in night-DOC release rates similar to those during daytime. Bioassays revealed major differences in the quality between day and night exudates: Night-DOC was utilized by bacterioplankton two times faster than day-DOC, but yielded a four times lower growth efficiency. Changes in benthic community composition were estimated to have resulted in a doubling of DOC release since 1973, due to an increasing abundance of benthic cyanobacterial mats (BCMs), with night-DOC release by BCMs and turf algae accounting for >50% of the total release over a diurnal cycle.Night-DOC released by BCMs and turf algae is likely an important driver in the microbialization of reefs by stimulating microbial respiration at the expense of energy and nutrient transfer to higher trophic levels via the microbial loop, thereby threatening the productivity and biodiversity of these unique ecosystems. Read the free Plain Language Summary for this article on the Journal blog.

El incremento de la liberación de materia orgánica disuelta (MOD) por parte de las algas se ha asociado con el crecimiento rápido pero ineficaz de microorganismos patógenos oportunistas y la continua degradación de los arrecifes coralinos. Los céspedes algales (consorcios de micro y macroalgas que suelen incluir cianobacterias) dominan las comunidades bentónicas de muchos arrecifes de todo el mundo. A diferencia de otras algas de arrecife que liberan predominantemente MOD durante el día, los céspedes algales que contienen cianobacterias pueden liberar adicionalmente grandes cantidades de MOD durante la noche. Sin embargo, esta liberación nocturna de MOD y su potencial contribución a la microbialización de los arrecifes aún falta por ser investigada.En primer lugar, investigamos la existencia de condiciones de hipoxia en la interfase entre los céspedes algales y el agua, ya que la falta de oxígeno facilitaría la producción y liberación de productos intermedios de fermentación como MOD nocturna. En segundo lugar, cuantificamos la liberación de carbono orgánico disuelto (COD) por los céspedes algales durante el día y la noche, y se comprobó la calidad de los exudados diurnos y nocturnos como alimento para el bacterioplancton. Finalmente, las tasas de liberación de MOD de los céspedes algales se combinaron con las estimaciones de liberación de COD basadas en la composición de la comunidad bentónica en 1973 y 2013 para explorar cómo los cambios en la composición de la comunidad bentónica afectaron a la contribución de MOD nocturna y a su vez a la producción de COD en todo el arrecife.En ausencia de luz, se produjo inmediatamente un cambio rápido de condiciones sobresaturadas a condiciones hipóxicas en la interfaz entre los céspedes algales y el agua, lo que dio lugar a tasas de liberación de COD nocturnas similares a las diurnas. Los bioensayos revelaron importantes diferencias en la calidad de los exudados diurnos y nocturnos: el bacterioplancton utilizó el COD nocturno dos veces más rápido que el COD diurno, pero su eficiencia de crecimiento fue cuatro veces menor. Se estimó que los cambios en la composición de la comunidad bentónica han dado lugar a una duplicación de la liberación de MOD desde 1973 debido a la creciente abundancia de tapetes de cianobacterias bentónicas, y que la liberación nocturna de COD por parte de estos tapetes y los céspedes algales representa >50% de la liberación total durante un ciclo diurno.El COD nocturno que es liberado por los tapetes de cianobacterias bentónicas y los céspedes algales es probablemente un importante promotor de la microbialización de los arrecifes al estimular la respiración microbiana a expensas de la transferencia de energía y nutrientes a los niveles tróficos superiores a través del bucle microbiano y, por tanto, amenaza la productividad y la biodiversidad de estos ecosistemas únicos.

Sponge holobionts shift their prokaryotic communities and antimicrobial activity from shallow to lower mesophotic depths.

In this study, we used 16S rRNA gene amplicon sequencing to investigate prokaryotic community composition of the Caribbean sponges Xestospongia muta and Agelas sventres from three depth ranges: < 30 m (shallow), 30-60 m (upper mesophotic), and 60-90 m (lower mesophotic). The prokaryotic community in shallow samples of X. muta was enriched in Cyanobacteria, Chloroflexota, and Crenarchaeota compared to samples from mesophotic depths, while mesophotic samples of X. muta were enriched in Acidobacteriota. For A. sventres, relative abundance of Acidobacteriota, Chloroflexota, and Gammaproteobacteria was higher in shallow samples, while Proteobacteria and Crenarchaeota were enriched in mesophotic A. sventres samples. Antimicrobial activity was evaluated by screening crude extracts of sponges against a set of Gram-positive and Gram-negative bacteria, a yeast, and an oomycete. Antibacterial activities from crude extracts of shallow sponge individuals were generally higher than observed from mesophotic individuals, that showed limited or no antibacterial activities. Conversely, the highest anti-oomycete activity was found from crude extracts of X. muta individuals from lower mesophotic depth, but without a clear pattern across the depth gradient. These results indicate that sponge-associated prokaryotic communities and the antimicrobial activity of sponges change within species across a depth gradient from shallow to mesophotic depth.

Sponges sneeze mucus to shed particulate waste from their seawater inlet pores.

Sponges, among the oldest extant multicellular organisms on Earth,1 play a key role in the cycling of nutrients in many aquatic ecosystems.2-5 They need to employ strategies to prevent clogging of their internal filter system by solid wastes,6-8 but self-cleaning mechanisms are largely unknown. It is commonly assumed that sponges remove solid waste with the outflowing water through distinct outflow openings (oscula).3,9 Here, we present time-lapse video footage and analyses of sponge waste revealing a completely different mechanism of particle removal in the Caribbean tube sponge Aplysina archeri. This sponge actively moves particle-trapping mucus against the direction of its internal water flow and ejects it into the surrounding water from its seawater inlet pores (ostia) through periodic surface contractions that have been described earlier as "sneezing."10,11 Visually, it appears as if the sponge is continuously streaming mucus-embedded particles and sneezes to shed this particulate waste, resulting in a notable flux of detritus that is actively consumed by sponge-associated fauna. The new data are used to estimate production of detritus for this abundant sponge on Caribbean coral reefs. Last, we discuss why waste removal from the sponge inhalant pores may be a common feature among sponges and compare the process in sponges to equivalent mechanisms of mucus transport in other animals, including humans.

Choose Wisely: Surgical Selection of Candidates for Outpatient Anterior Cervical Surgery Based on Early Complications Among Inpatients.

BACKGROUND: Anterior cervical discectomy and fusion (ACDF) and cervical disc arthroplasty (CDA) are attractive targets for transition to the outpatient setting. We assessed the prevalence of rapid responses and major complications in the inpatient setting following 1 or 2-level ACDFs and CDAs. We evaluated factors that may place patients at greater risk for a rapid response or a postoperative complication. METHODS: This was an institutional review board-approved, retrospective cohort study of adults undergoing 1 or 2-level ACDF or CDA at 1 hospital over a 2-year period (2018 and 2019). Data on patient demographic characteristics, surgical procedures, and comorbidities were collected. Rapid response events were identified by hospital floor staff and involved acute changes in a patient's clinical condition. Complications were events that were life-threatening, required an intervention, or led to delayed hospital discharge. RESULTS: In this study, 1,040 patients were included: 888 underwent ACDF and 152 underwent CDA. Thirty-six patients (3.5%) experienced a rapid response event; 22% occurred >24 hours after extubation. Patients having a rapid response event had a significantly higher risk of developing a complication (risk ratio, 10; p < 0.01) and had a significantly longer hospital stay. Twenty-four patients (2.3%) experienced acute complications; 71% occurred >6 hours after extubation. Patients with a complication were older and more likely to be current or former smokers, have chronic obstructive pulmonary disease, have asthma, and have an American Society of Anesthesiologists (ASA) score of >2. The length of the surgical procedure was significantly longer in patients who developed a complication. All patients who developed dysphagia had a surgical procedure involving C4-C5 or more cephalad. Patients with a rapid response event or complication were more commonly undergoing revision surgical procedures. CONCLUSIONS: Rapid response and complications are uncommon following 1 or 2-level ACDFs or CDAs but portend a longer hospital stay and increased morbidity. Revision surgical procedures place patients at higher risk for rapid responses and complications. Additionally, older patients, patients with chronic obstructive pulmonary disease or asthma, patients who are current or former smokers, and patients who have an ASA score of ≥3 are at increased risk for postoperative complications. LEVEL OF EVIDENCE: Prognostic Level III . See Instructions for Authors for a complete description of levels of evidence.

Surface flow for colonial integration in reef-building corals.

Reef-building corals are endangered animals with a complex colonial organization. Physiological mechanisms connecting multiple polyps and integrating them into a coral colony are still enigmatic. Using live imaging, particle tracking, and mathematical modeling, we reveal how corals connect individual polyps and form integrated polyp groups via species-specific, complex, and stable networks of currents at their surface. These currents involve surface mucus of different concentrations, which regulate joint feeding of the colony. Inside the coral, within the gastrovascular system, we expose the complexity of bidirectional branching streams that connect individual polyps. This system of canals extends the surface area by 4-fold and might improve communication, nutrient supply, and symbiont transfer. Thus, individual polyps integrate via complex liquid dynamics on the surface and inside the colony.

Implications of 2D versus 3D surveys to measure the abundance and composition of benthic coral reef communities.

A paramount challenge in coral reef ecology is to estimate the abundance and composition of the communities residing in such complex ecosystems. Traditional 2D projected surface cover estimates neglect the 3D structure of reefs and reef organisms, overlook communities residing in cryptic reef habitats (e.g., overhangs, cavities), and thus may fail to represent biomass estimates needed to assess trophic ecology and reef function. Here, we surveyed the 3D surface cover, biovolume, and biomass (i.e., ash-free dry weight) of all major benthic taxa on 12 coral reef stations on the island of Curaçao (Southern Caribbean) using structure-from-motion photogrammetry, coral point counts, in situ measurements, and elemental analysis. We then compared our 3D benthic community estimates to corresponding estimates of traditional 2D projected surface cover to explore the differences in benthic community composition using different metrics. Overall, 2D cover was dominated (52 ± 2%, mean ± SE) by non-calcifying phototrophs (macroalgae, turf algae, benthic cyanobacterial mats), but their contribution to total reef biomass was minor (3.2 ± 0.6%). In contrast, coral cover (32 ± 2%) more closely resembled coral biomass (27 ± 6%). The relative contribution of erect organisms, such as gorgonians and massive sponges, to 2D cover was twofold and 11-fold lower, respectively, than their contribution to reef biomass. Cryptic surface area (3.3 ± 0.2 m2 m-2 planar reef) comprised half of the total reef substrate, rendering two thirds of coralline algae and almost all encrusting sponges (99.8%) undetected in traditional assessments. Yet, encrusting sponges dominated reef biomass (35 ± 18%). Based on our quantification of exposed and cryptic reef communities using different metrics, we suggest adjustments to current monitoring approaches and highlight ramifications for evaluating the ecological contributions of different taxa to overall reef function. To this end, our metric conversions can complement other benthic assessments to generate non-invasive estimates of the biovolume, biomass, and elemental composition (i.e., standing stocks of organic carbon and nitrogen) of Caribbean coral reef communities. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00338-021-02118-6.

Space-filling and benthic competition on coral reefs.

Reef-building corals are ecosystem engineers that compete with other benthic organisms for space and resources. Corals harvest energy through their surface by photosynthesis and heterotrophic feeding, and they divert part of this energy to defend their outer colony perimeter against competitors. Here, we hypothesized that corals with a larger space-filling surface and smaller perimeters increase energy gain while reducing the exposure to competitors. This predicted an association between these two geometric properties of corals and the competitive outcome against other benthic organisms. To test the prediction, fifty coral colonies from the Caribbean island of Curaçao were rendered using digital 3D and 2D reconstructions. The surface areas, perimeters, box-counting dimensions (as a proxy of surface and perimeter space-filling), and other geometric properties were extracted and analyzed with respect to the percentage of the perimeter losing or winning against competitors based on the coral tissue apparent growth or damage. The increase in surface space-filling dimension was the only significant single indicator of coral winning outcomes, but the combination of surface space-filling dimension with perimeter length increased the statistical prediction of coral competition outcomes. Corals with larger surface space-filling dimensions (Ds > 2) and smaller perimeters displayed more winning outcomes, confirming the initial hypothesis. We propose that the space-filling property of coral surfaces complemented with other proxies of coral competitiveness, such as life history traits, will provide a more accurate quantitative characterization of coral competition outcomes on coral reefs. This framework also applies to other organisms or ecological systems that rely on complex surfaces to obtain energy for competition.

Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design.

Structure-based antibody and antigen design has advanced greatly in recent years, due not only to the increasing availability of experimentally determined structures but also to improved computational methods for both prediction and design. Constant improvements in performance within the Rosetta software suite for biomolecular modeling have given rise to a greater breadth of structure prediction, including docking and design application cases for antibody and antigen modeling. Here, we present an overview of current protocols for antibody and antigen modeling using Rosetta and exemplify those by detailed tutorials originally developed for a Rosetta workshop at Vanderbilt University. These tutorials cover antibody structure prediction, docking, and design and antigen design strategies, including the addition of glycans in Rosetta. We expect that these materials will allow novice users to apply Rosetta in their own projects for modeling antibodies and antigens.

Differential processing of dissolved and particulate organic matter by deep-sea sponges and their microbial symbionts.

Deep-sea sponges create hotspots of biodiversity and biological activity in the otherwise barren deep-sea. However, it remains elusive how sponge hosts and their microbial symbionts acquire and process food in these food-limited environments. Therefore, we traced the processing (i.e. assimilation and respiration) of 13C- and 15N-enriched dissolved organic matter (DOM) and bacteria by three dominant North Atlantic deep-sea sponges: the high microbial abundance (HMA) demosponge Geodia barretti, the low microbial abundance (LMA) demosponge Hymedesmia paupertas, and the LMA hexactinellid Vazella pourtalesii. We also assessed the assimilation of both food sources into sponge- and bacteria-specific phospholipid-derived fatty acid (PLFA) biomarkers. All sponges were capable of assimilating DOM as well as bacteria. However, processing of the two food sources differed considerably between the tested species: the DOM assimilation-to-respiration efficiency was highest for the HMA sponge, yet uptake rates were 4-5 times lower compared to LMA sponges. In contrast, bacteria were assimilated most efficiently and at the highest rate by the hexactinellid compared to the demosponges. Our results indicate that phylogeny and functional traits (e.g., abundance of microbial symbionts, morphology) influence food preferences and diet composition of sponges, which further helps to understand their role as key ecosystem engineers of deep-sea habitats.

Product inhibition in nucleophilic aromatic substitution through DPPPent-supported π-arene catalysis.

Nucleophilic aromatic substitution (SNAr) of fluorobenzene by morpholine at a bis(diphenylphosphino)pentane-supported ruthenim complex is investigated as a model system for π-arene catalysis through the synthesis and full characterization of proposed intermediates. The SNAr step proceeds quickly at room temperature, however the product N-phenylmorpholine binds tightly to the ruthenium ion. In the case examined, the thermodynamics of arene binding favor product N-phenylmorpholine over fluorobenzene binding by a factor of 2000, corresponding to significant product inhibition. Observations of the catalyst resting state support this hypothesis and demonstrate an additive-controlled role for a previously-proposed ligand cyclometalation.

Potently neutralizing and protective human antibodies against SARS-CoV-2.

The ongoing pandemic of coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a major threat to global health1 and the medical countermeasures available so far are limited2,3. Moreover, we currently lack a thorough understanding of the mechanisms of humoral immunity to SARS-CoV-24. Here we analyse a large panel of human monoclonal antibodies that target the spike (S) glycoprotein5, and identify several that exhibit potent neutralizing activity and fully block the receptor-binding domain of the S protein (SRBD) from interacting with human angiotensin-converting enzyme 2 (ACE2). Using competition-binding, structural and functional studies, we show that the monoclonal antibodies can be clustered into classes that recognize distinct epitopes on the SRBD, as well as distinct conformational states of the S trimer. Two potently neutralizing monoclonal antibodies, COV2-2196 and COV2-2130, which recognize non-overlapping sites, bound simultaneously to the S protein and neutralized wild-type SARS-CoV-2 virus in a synergistic manner. In two mouse models of SARS-CoV-2 infection, passive transfer of COV2-2196, COV2-2130 or a combination of both of these antibodies protected mice from weight loss and reduced the viral burden and levels of inflammation in the lungs. In addition, passive transfer of either of two of the most potent ACE2-blocking monoclonal antibodies (COV2-2196 or COV2-2381) as monotherapy protected rhesus macaques from SARS-CoV-2 infection. These results identify protective epitopes on the SRBD and provide a structure-based framework for rational vaccine design and the selection of robust immunotherapeutic agents.

Comparative modeling and docking of chemokine-receptor interactions with Rosetta.

Chemokine receptors are a subset of G protein-coupled receptors defined by the distinct property of binding small protein ligands in the chemokine family. Chemokine receptors recognize their ligands by a mechanism that is distinct from other class A GPCRs that bind peptides or small molecules. For this reason, structural information on other ligand-GPCR interactions are only indirectly relevant to understanding the chemokine receptor interface. Additionally, the experimentally determined structures of chemokine-GPCR complexes represent less than 3% of the known interactions of this complex, multi-ligand/multi-receptor network. To enable predictive modeling of the remaining 97% of interactions, a general in silico protocol was designed to utilize existing chemokine receptor crystal structures, co-crystal structures, and NMR ensembles of chemokines bound to receptor fragments. This protocol was benchmarked on the ability to predict each of the three published co-crystal structures, while being blinded to the target structure. Averaging ensembles selected from the top-ranking models reproduced up to 84% of the intermolecular contacts found in the crystal structure, with the lowest Cα-RMSD of the complex at 3.3 Å. The chemokine receptor N-terminus, unresolved in crystal structures, was included in the modeling and recapitulates contacts with known sulfotyrosine binding pockets seen in structures derived from experimental NMR data. This benchmarking experiment suggests that realistic homology models of chemokine-GPCR complexes can be generated by leveraging current structural data.

Symptomatic pseudarthrosis requiring revision surgery after 1- or 2-level ACDF with plating: peek versus allograft.

BACKGROUND: Polyetheretherketone (PEEK) and machined allograft interbody spacers are among devices used as fusion adjuncts in anterior cervical discectomy and fusion (ACDF). Most results are good to excellent but some patients develop pseudarthrosis. We compared the reoperation rates for pseudarthrosis following 1- or 2-level ACDF with PEEK or allograft cages. METHODS: This was a retrospective cohort study. We reviewed patients who underwent 1- or 2-level ACDF. The rate of subsequent surgery for pseudarthrosis was calculated for cases confirmed by computerized tomography. Patient-reported outcomes were collected at post-index surgery follow-up and post-revision ACDF follow-up. Radiographic parameters were assessed at a minimum of 1-year post-op on all patients. RESULTS: Two hundred and nine patients were included: 167 received allograft and 42 received PEEK. Subsidence was demonstrated in 31% of allograft and 29% of PEEK patients. There were no significant differences in clinical outcomes between allograft and PEEK groups. Clinical outcomes were not adversely affected by subsidence. Reoperation for pseudarthrosis was performed in 8% of allograft patients and 14% of PEEK patients (not statistically different). Improvement in patient-reported outcome was significantly better for patients without symptomatic post-operative pseudarthrosis. CONCLUSIONS: Both allograft and PEEK spacers are acceptable options for ACDF surgery. Similar clinical outcomes and rates of radiographic subsidence were found. Subsidence was not a factor in clinical outcomes. Reoperation for pseudarthrosis was associated with poor outcomes. A higher incidence of revision for symptomatic pseudarthrosis occurred in the PEEK group, but this was not statistically significant.

Modeling the complete chemokine-receptor interaction.

Chemokines are soluble, secreted proteins that induce chemotaxis of leukocytes and other cells. Migratory cells can sense the chemokine concentration gradient following chemokine binding and activation of chemokine receptors, a subset of the G protein-coupled receptor (GPCR) superfamily. Chemokine receptor signaling plays a central role in cell migration during inflammatory responses as well as in cancer and other diseases. Given their important role in mediating essential pathologic and physiologic processes, chemokines and their receptors are attractive targets for therapeutic development. A better understanding of the molecular basis of chemokine-GPCR interactions will aid in the understanding of the mechanistic basis for chemokine function in disease-related processes, as well as aid in the design of new therapeutics. High resolution protein structures are critical for determining these mechanisms and investigating the interactions between approximately 50 chemokines and 20 chemokine receptors. Currently, three unique structures of chemokine-GPCR complexes have been determined and have greatly broadened our knowledge of this large protein-protein interaction. While these structures represent only a small fraction of clinically relevant chemokines and receptors, they can be exploited as scaffolds for homology modeling to understand the chemokine-GPCR interactions. This chapter presents a specialized methodology to construct and validate models of chemokine-GPCR complexes using the Rosetta software suite.

Posterolateral Versus Transforaminal Interbody L4/5 Fusion: Correlation With Subsequent Surgery.

STUDY DESIGN: This is a retrospective cohort study. OBJECTIVE: To compare posterolateral versus transforaminal interbody fusion (PLF vs. PLF+TLIF) of the L4/5 segment regarding rates of subsequent surgery, clinical and radiographic parameters, and patient satisfaction. SUMMARY OF BACKGROUND DATA: Surgical treatment of lumbar stenosis, decompression with or without fusion, is an efficacious treatment in select patients. Reoperation is thought to be a problem after lumbar fusion. Despite multiple studies, the fusion method that minimizes the need for subsequent surgery has yet to be determined. MATERIALS AND METHODS: A retrospective cohort study was conducted on 89 patients who had an isolated L4/5 decompression and fusion, from January 2006 to 2012. All patients had stenosis and degenerative spondylolisthesis at the L4/5 level. All surgeries were performed at a single center, using either PLF (31 patients) or PLF+TLIF (58 patients) techniques. Preoperative and postoperative patient-reported outcome measures (Oswestry disability index, visual analog scale back pain, visual analog scale leg pain) and radiographic parameters (L4/5 lordosis and overall lumbar lordosis) were measured. Patient satisfaction was acquired via a questionnaire. Chart reviews and patient questionnaires were used to determine the incidence of subsequent lumbar surgery over a minimum follow-up of 5 years. RESULTS: At an average of 8.7 years follow-up, 2 of 31 patients in the PLF group had subsequent lumbar surgery, compared with 16 of 58 patients in the PLF+TLIF group (6% vs. 28%; P=0.02). There were no significant differences between groups with respect to sex, age, body mass index, tobacco, perioperative measures, patient-reported outcomes, or radiographic parameters (P>0.05). CONCLUSIONS: Both PLF and PLF+TLIF are effective fusion methods for L4/5 stenosis and spondylolisthesis. In this study, patients treated with PLF were less likely to undergo a subsequent lumbar surgery. More research is needed to determine which factors influence whether PLF or PLF+TLIF should be used in these patients. LEVEL OF EVIDENCE: Level III.

Spatio-temporal variation in stable isotope signatures (δ13C and δ15N) of sponges on the Saba Bank.

Sponges are ubiquitous on coral reefs, mostly long lived and therefore adaptive to changing environmental conditions. They feed on organic matter withdrawn from the passing water and they may harbor microorganisms (endosymbionts), which contribute to their nutrition. Their diets and stable isotope (SI) fractionation determine the SI signature of the sponge holobiont. Little is known of spatio-temporal variations in SI signatures of δ13C and δ15N in tropical sponges and whether they reflect variations in the environment. We investigated the SI signatures of seven common sponge species with different functional traits and their potential food sources between 15 and 32 m depth along the S-SE and E-NE side of the Saba Bank, Eastern Caribbean, in October 2011 and October 2013. SI signatures differed significantly between most sponge species, both in mean values and in variation, indicating different food preferences and/or fractionation, inferring sponge species-specific isotopic niche spaces. In 2011, all sponge species at the S-SE side were enriched in d13C compared to the E-NE side. In 2013, SI signatures of sponges did not differ between the two sides and were overall lighter in δ13C and δ15N than in 2011. Observed spatio-temporal changes in SI in sponges could not be attributed to changes in the SI signatures of their potential food sources, which remained stable with different SI signatures of pelagic (particulate organic matter (POM): δ13C -24.9‰, δ15N +4.3‰) and benthic-derived food (macroalgae: δ13C -15.4‰, δ15N +0.8‰). Enriched δ13C signatures in sponges at the S-SE side in 2011 are proposed to be attributed to predominantly feeding on benthic-derived C. This interpretation was supported by significant differences in water mass constituents between sides in October 2011. Elevated NO3 and dissolved organic matter concentrations point toward a stronger reef signal in reef overlying water at the S-SE than N-NE side of the Bank in 2011. The depletions of δ13C and δ15N in sponges in October 2013 compared to October 2011 concurred with significantly elevated POM concentrations. The contemporaneous decrease in δ15N suggests that sponges obtain their N mostly from benthic-derived food with a lower δ15N than pelagic food. Average proportional feeding on available sources varied between sponge species and ranged from 20% to 50% for benthic and 50% to 80% for pelagic-derived food, assuming trophic enrichment factors of 0.5‰ ± sd 0.5 for δ13C and 3‰ ± sd 0.5 for δ15N for sponges. We suggest that observed variation of SI in sponges between sides and years were the result of shifts in the proportion of ingested benthic- and pelagic-derived organic matter driven by environmental changes. We show that sponge SI signatures reflect environmental variability in space and time on the Saba Bank and that SI of sponges irrespective of their species-specific traits move in a similar direction in response to these environmental changes.

Holistic Approach to Partial Covalent Interactions in Protein Structure Prediction and Design with Rosetta.

Partial covalent interactions (PCIs) in proteins, which include hydrogen bonds, salt bridges, cation-π, and π-π interactions, contribute to thermodynamic stability and facilitate interactions with other biomolecules. Several score functions have been developed within the Rosetta protein modeling framework that identify and evaluate these PCIs through analyzing the geometry between participating atoms. However, we hypothesize that PCIs can be unified through a simplified electron orbital representation. To test this hypothesis, we have introduced orbital based chemical descriptors for PCIs into Rosetta, called the PCI score function. Optimal geometries for the PCIs are derived from a statistical analysis of high-quality protein structures obtained from the Protein Data Bank (PDB), and the relative orientation of electron deficient hydrogen atoms and electron-rich lone pair or π orbitals are evaluated. We demonstrate that nativelike geometries of hydrogen bonds, salt bridges, cation-π, and π-π interactions are recapitulated during minimization of protein conformation. The packing density of tested protein structures increased from the standard score function from 0.62 to 0.64, closer to the native value of 0.70. Overall, rotamer recovery improved when using the PCI score function (75%) as compared to the standard Rosetta score function (74%). The PCI score function represents an improvement over the standard Rosetta score function for protein model scoring; in addition, it provides a platform for future directions in the analysis of small molecule to protein interactions, which depend on partial covalent interactions.