Combinatorial materials research applied to the development of new surface coatings IV. A high-throughput bacterial biofilm retention and retraction assay for screening fouling-release performance of coatings

Abstract

A high-throughput bacterial biofilm retention screening method has been augmented to facilitate the rapid analysis and down-selection of fouling-release coatings for identification of promising candidates. Coatings were cast in modified 24-well tissue culture plates and inoculated with the marine bacterium Cytophaga lytica for attachment and biofilm growth. Biofilms retained after rinsing with deionised water were dried at ambient laboratory conditions. During the drying process, retained biofilms retracted through a surface de-wetting phenomenon on the hydrophobic silicone surfaces. The retracted biofilms were stained with crystal violet, imaged, and analysed for percentage coverage. Two sets of experimental fouling-release coatings were analysed with the high-throughput biofilm retention and retraction assay (HTBRRA). The first set consisted of a series of model polysiloxane coatings that were systematically varied with respect to ratios of low and high MW silanol-terminated PDMS, level of cross-linker, and amount of silicone oil. The second set consisted of cross-linked PDMS-polyurethane coatings varied with respect to the MW of the PDMS and end group functionality. For the model polysiloxane coatings, HTBRRA results were compared to data obtained from field immersion testing at the Indian River Lagoon at the Florida Institute of Technology. The percentage coverage calculations of retracted biofilms correlated well to barnacle adhesion strength in the field (R² = 0.82) and accurately identified the best and poorest performing coating compositions. For the cross-linked PDMS-polyurethane coatings, the HTBRRA results were compared to combinatorial pseudobarnacle pull-off adhesion data and good agreement in performance was observed. Details of the developed assay and its implications in the rapid discovery of new fouling-release coatings are discussed.     

Improved two‐stage group sequential procedures for testing a secondary endpoint after the primary endpoint achieves significance

In two‐stage group sequential trials with a primary and a secondary endpoint, the overall type I error rate for the primary endpoint is often controlled by an α‐level boundary, such as an O'Brien‐Fleming or Pocock boundary. Following a hierarchical testing sequence, the secondary endpoint is tested only if the primary endpoint achieves statistical significance either at an interim analysis or at the final analysis. To control the type I error rate for the secondary endpoint, this is tested using a Bonferroni procedure or any α‐level group sequential method. In comparison with marginal testing, there is an overall power loss for the test of the secondary endpoint since a claim of a positive result depends on the significance of the primary endpoint in the hierarchical testing sequence. We propose two group sequential testing procedures with improved secondary power: the improved Bonferroni procedure and the improved Pocock procedure. The proposed procedures use the correlation between the interim and final statistics for the secondary endpoint while applying graphical approaches to transfer the significance level from the primary endpoint to the secondary endpoint. The procedures control the familywise error rate (FWER) strongly by construction and this is confirmed via simulation. We also compare the proposed procedures with other commonly used group sequential procedures in terms of control of the FWER and the power of rejecting the secondary hypothesis. An example is provided to illustrate the procedures.     

Dynamic combinatorial libraries of artificial repeat proteins

Repeat proteins are found in almost all cellular systems, where they are involved in diverse molecular recognition processes. Recent studies have suggested that de novo designed repeat proteins may serve as universal binders, and might potentially be used as practical alternative to antibodies. We describe here a novel chemical methodology for producing small libraries of repeat proteins, and screening in parallel the ligand binding of library members. The first stage of this research involved the total synthesis of a consensus-based three-repeat tetratricopeptide (TPR) protein (～14 kDa), via sequential attachment of the respective peptides. Despite the effectiveness of the synthesis and ligation steps, this method was found to be too demanding for the production of proteins containing variable number of repeats. Additionally, the analysis of binding of the individual proteins was time consuming. Therefore, we designed and prepared novel dynamic combinatorial libraries (DCLs), and show that their equilibration can facilitate the formation of TPR proteins containing up to eight repeating units. Interestingly, equilibration of the library building blocks in the presence of the biologically relevant ligands, Hsp90 and Hsp70, induced their oligomerization into forming more of the proteins with large recognition surfaces. We suggest that this work presents a novel simple and rapid tool for the simultaneous screening of protein mixtures with variable binding surfaces, and for identifying new binders for ligands of interest.     

无充气腋窝入路腔镜下单侧甲状腺癌根治术与开放性手术的疗效比较及对免疫功能和颈部功能的影响

摘要 目的：比较无充气腋窝入路腔镜下单侧甲状腺癌根治术与开放性手术的疗效及对免疫功能和颈部功能的影响。方法：回顾性分析我院2020年8月～2021年8月期间收治的行单侧甲状腺癌根治术患者80例的临床资料。根据手术方式的不同将患者分为开放组（开放性手术）和腔镜组（无充气腋窝入路腔镜下单侧甲状腺癌根治术）,例数分别为37例和43例。对比两组疗效、免疫功能、颈部功能、美容学满意度和并发症情况。结果：与开放组相比,腔镜组术中出血量更少,手术时间、住院时间更长,引流液总量更多（P<0.05）,两组中央组淋巴结清扫数组间对比无统计学差异（P>0.05）。两组CD3⁺、CD4⁺、CD4⁺/CD8⁺下降,但腔镜组高于开放组;CD8+升高,但腔镜组低于开放组（P<0.05）。两组术后3d视觉疼痛模拟评分法（VAS）评分、颈部损伤指数对比,差异无统计学意义（P>0.05）。腔镜组吞咽障碍指数低于开放组（P<0.05）。腔镜组的总满意率高于开放组（P<0.05）。两组并发症发生率组间对比无统计学差异（P>0.05）。结论：与开放性手术治疗单侧甲状腺癌相比,无充气腋窝入路腔镜下单侧甲状腺癌根治术的手术时间和住院时间虽然延长,但其对患者免疫功能影响更轻,同时还可减轻患者吞咽障碍,获得更好的美容学满意度。     

Using dynamic sustainability indicators to assess environmental policy measures in Biosphere Reserves

The assessment of different policy options represents a major tool for decision-makers in Biosphere Reserves, to develop more-resilient strategies for sustainable development and to visualise unintended consequences of these policies.In this work we analyse eight measures proposed by different agents in order to meet the main objectives of environmental sustainability, included in the Action Plan of the Fuerteventura Biosphere Reserve (Spain). We quantified the effects of these measures in terms of the sustainability thresholds of 10 environmental indicators, also proposed by the Action Plan, which was integrated in the Fuerteventura Biosphere Reserve dynamic model. Their behaviours under these measures allow determination of whether the objectives will be met in the period 2012–2025. Although some indicators would improve under these measures, fitting certain objectives, some negative effects on other indicators confirm the existence of trade-offs among these objectives. For instance, grazing limitation would improve the proportion of high-quality vegetation but would negatively affect the Egyptian vulture population, which would even fall below its sustainability threshold. The definition of thresholds for each indicator allows decision-makers to establish a way to prioritise among the eight measures analysed. The results show that these measures are insufficient to meet the sustainability thresholds of four indicators (the landscape indicator, the proportion of renewable energy, the per capita primary energy consumption and carbon dioxide emissions). Focusing on the remaining six indicators and following the rule “Threshold out, measure out”, seven out of the eight measures would exceed some thresholds and should be avoided. Only one option, aimed at growing fodder to feed cattle on restored traditional agricultural lands, would not exceed any of these thresholds. However, this measure also presents certain negative effects regarding indicators related to flagship species (the houbara habitat and the Egyptian vulture population), which would require compensation measures.     

Increased susceptibility to fungal disease accompanies adaptation to drought in Brassica rapa

Recent studies have demonstrated adaptive evolutionary responses to climate change, but little is known about how these responses may influence ecological interactions with other organisms, including natural enemies. We used a resurrection experiment in the greenhouse to examine the effect of evolutionary responses to drought on the susceptibility of Brassica rapa plants to a fungal pathogen, Alternaria brassicae. In agreement with previous studies in this population, we found an evolutionary shift to earlier flowering postdrought, which was previously shown to be adaptive. Here, we report the novel finding that postdrought descendant plants were also more susceptible to disease, indicating a rapid evolutionary shift to increased susceptibility. This was accompanied by an evolutionary shift to increased specific leaf area (thinner leaves) following drought. We found that flowering time and disease susceptibility displayed plastic responses to experimental drought treatments, but that this plasticity did not match the direction of evolution, indicating that plastic and evolutionary responses to changes in climate can be opposed. The observed evolutionary shift to increased disease susceptibility accompanying adaptation to drought provides evidence that even if populations can rapidly adapt in response to climate change, evolution in other traits may have ecological effects that could make species more vulnerable.     

Specific GFP-binding artificial proteins (αRep): a new tool for in?vitro to live cell applications

A family of artificial proteins, named αRep, based on a natural family of helical repeat was previously designed. αRep members are efficiently expressed, folded and extremely stable proteins. A large αRep library was constructed creating proteins with a randomized interaction surface. In the present study, we show that the αRep library is an efficient source of tailor-made specific proteins with direct applications in biochemistry and cell biology. From this library, we selected by phage display αRep binders with nanomolar dissociation constants against the GFP. The structures of two independent αRep binders in complex with the GFP target were solved by X-ray crystallography revealing two totally different binding modes. The affinity of the selected αReps for GFP proved sufficient for practically useful applications such as pull-down experiments. αReps are disulfide free proteins and are efficiently and functionally expressed in eukaryotic cells: GFP-specific αReps are clearly sequestrated by their cognate target protein addressed to various cell compartments. These results suggest that αRep proteins with tailor-made specificity can be selected and used in living cells to track, modulate or interfere with intracellular processes.     

神经内镜与显微镜下经鼻蝶入路手术切除垂体腺瘤的临床疗效比较及术中出现脑脊液漏的危险因素分析

摘要 目的：对比垂体腺瘤患者采用显微镜或神经内镜下经鼻蝶入路手术切除后的临床疗效,分析术中出现脑脊液漏的危险因素。方法：回顾性分析2018年3月~2022年2月期间来我院接受手术治疗的178例垂体腺瘤患者的临床资料。根据采用手术器械的不同将178例患者分为A组（显微镜,n=91）和B组（神经内镜,n=87）。比较两组的肿瘤有效切除率、临床指标、术中脑脊液漏发生率及术后并发症发生率。根据术中是否发生脑脊液漏分为脑脊液漏组和无脑脊液漏组。经单因素和多因素Logistic回归分析患者术中发生脑脊液漏的危险因素。结果：B组的手术时间、住院时间短于A组,术中出血量少于A组（P<0.05）。A组、B组的肿瘤有效切除率组间对比,无统计学差异（P>0.05）。B组术中脑脊液漏发生率、术后并发症发生率低于A组（P<0.05）。垂体腺瘤患者术中发生脑脊液漏与再次手术、肿瘤大小、年龄、肿瘤质地、美国麻醉医师协会（ASA）分级有关（P<0.05）。肿瘤大小为巨大腺瘤、再次手术、肿瘤质地为韧是垂体腺瘤患者术中发生脑脊液漏的危险因素（P<0.05）。结论：显微镜与神经内镜下经鼻蝶入路手术切除垂体腺瘤,治疗效果相当,但神经内镜下手术可缩短手术时间、住院时间,减少术中出血量,降低术中脑脊液漏发生率、术后并发症发生率。此外,肿瘤大小为巨大腺瘤、再次手术、肿瘤质地为韧是垂体腺瘤患者术中发生脑脊液漏的危险因素。     

Directed discovery of bivalent peptide ligands to an SH3 domain

The Caenorhabditis elegans SEM-5 SH3 domains recognize proline-rich peptide segments with modest affinity. We developed a bivalent peptide ligand that contains a naturally occurring proline-rich binding sequence, tethered by a glycine linker to a disulfide-closed loop segment containing six variable residues. The glycine linker allows the loop segment to explore regions of greatest diversity in sequence and structure of the SH3 domain: the RT and n-Src loops. The bivalent ligand was optimized using phage display, leading to a peptide (PP-G(4)-L) with 1000-fold increased affinity for the SEM-5 C-terminal SH3 domain over that of a natural ligand. NMR analysis of the complex confirms that the peptide loop segment is targeted to the RT and n-Src loops and parts of the beta-sheet scaffold of this SH3 domain. This binding region is comparable to that targeted by a natural non-PXXP peptide to the p67(phox) SH3 domain, a region not known to be targeted in the Grb2 SH3 domain family. PP-G(4)-L may aid in the discovery of additional binding partners of Grb2 family SH3 domains.     

Candidatus "Scalindua brodae", sp. nov., Candidatus "Scalindua wagneri", sp. nov., two new species of anaerobic ammonium oxidizing bacteria

Anaerobic ammonium oxidation (anammox) is both a promising process in wastewater treatment and a long overlooked microbial physiology that can contribute significantly to biological nitrogen cycling in the world's oceans. Anammox is mediated by a monophyletic group of bacteria that branches deeply in the Planctomycetales. Here we describe a new genus and species of anaerobic ammonium oxidizing planctomycetes, discovered in a wastewater treatment plant (wwtp) treating landfill leachate in Pitsea, UK. The biomass from this wwtp showed high anammox activity (5.0 +/- 0.5 nmol/mg protein/min) and produced hydrazine from hydroxylamine, one of the unique features of anammox bacteria. Eight new planctomycete 16S rRNA gene sequences were present in the 16S rRNA gene clone library generated from the biomass. Four of these were affiliated to known anammox 16S rRNA gene sequences, but branched much closer to the root of the planctomycete line of descent. Fluorescence in situ hybridization (FISH) with oligonucleotide probes specific for these new sequences showed that two species (belonging to the same genus) together made up > 99% of the planctomycete population which constituted 20% of the total microbial community. The identification of these organisms as typical anammox bacteria was confirmed with electron microscopy and lipid analysis. The new species, provisionally named Candidatus "Scalindua brodae" and "Scalindua wagneri" considerably extend the biodiversity of the anammox lineage on the 16S rRNA gene level, but otherwise resemble known anammox bacteria. Simultaneously, another new species of the same genus, Candidatus "Scalindua sorokinii", was detected in the water column of the Black Sea, making this genus the most widespread of all anammox bacteria described so far.