Geographic Tools for Eradication Programs of Insular Non-native Mammals

Non-native mammals are major drivers of ecosystem change and biodiversity loss; this is especially apparent on islands. However, techniques exist to remove non-native mammals, providing a powerful conservation tool. Conservation practitioners are now targeting larger islands for restoration. Leveraging existing and developing new techniques and technologies will prove critical to successful eradications on large islands. Using the removal of introduced goats (Capra hircus) from Santiago Island, Galápagos as a case study, we present a suite of Geographic Information System (GIS) tools that aid island conservation actions. GIS tools were incorporated into the three phases of the eradication campaign: planning, hunting, and monitoring. Further, these tools were adopted for three eradication techniques: ground-based hunting, aerial hunting by helicopter, and Judas goats. These geographic approaches provide a foundation for statistical, spatial, and economic analyses that should increase the capability and efficiency of removal campaigns. Given limited conservation funds and the dire status of many insular species, efficiently removing non-native mammals from islands is of paramount global conservation importance.     

Cardiovascular implantable electronic device lead removal in a resource-constrained setting: A single-center experience from India

BackgroundData from large-volume centers in developed countries, using dedicated tools, show a high success rate with a good safety record for the percutaneous lead removal procedure. However, there are constraints to replicate the results in a resource-poor setting and there is limited data from India.MethodsWe retrospectively analyzed lead removal procedures performed in our institution from 2008 to 2019.ResultsSeventy-five patients underwent percutaneous removal of 138 leads. Of these, 44 procedures and 80 leads qualified as extraction with a median dwell time of 52.1 (IQR 28.2–117.2) months. Overall, 33/44 (75.0%) procedures were successful and 65/80 (81.2%) leads were successfully extracted. Manual traction was successful in the extraction of 44/57 (77.2%) leads. All leads implanted less than 2.7 years could be removed with manual traction alone. Specialized tools were used in 23 leads and 21 (91.3%) of those could be successfully extracted. Inability to use dedicated tools was an independent predictor of procedural failure (adjusted OR 14.0; 95% CI 1.8–110.2; p-value 0.012). Right-sided implant (adjusted OR 12.6; 95% CI 1.3–119.5; p-value 0.027) was also independently associated with failure. There was 1 death (1.3%) and minor complications occurred in 6 (8.0%) patients.ConclusionsIn a resource-limited setting, percutaneous lead extraction of predominantly pacemaker leads by manual traction methods achieved success in extracting about three-fourths of the leads. Inability to use specialized tools was the main factor limiting success. The complication rate was low.     

The use of biological activities to monitor the removal of fuel contaminants—perspective for monitoring hydrocarbon contamination: a review

Soil biological activities are vital for the restoration of soil contaminated with hydrocarbons. Their role includes the biotransformation of petroleum compounds into harmless compounds. In this paper, the use of biological activities as potential monitoring tools or bioindicators during bioremediation of hydrocarbon-contaminated soil are reviewed. The use of biological activities as bioindicators of hydrocarbon removal in soil has been reported with variable success. This variability can be attributed partially to the spatial variability of soil properties, which undoubtedly plays a role in the exposure of organisms to contaminants. Widely used bioindicators have been enzyme activities, seed germination, earthworm survival and microorganisms or microbial bioluminescence. A mixture of some successful utilization of biological activities and several failures, and inconsistencies reported, show that at this stage there is no general guarantee of successful utilization of biological activities as monitoring tools. Wherever possible, the use of biological activities as bioindicators of hydrocarbon removal must be used to complement existing traditional monitoring tools.     

Carbon,nitrogen and phosphorus removal mechanisms of aerobic granules

Aerobic granules are the potential tools to develop modern wastewater treatment technologies with improved nutrient removal efficiency. These granules have several promising advantages over conventional activated sludge-based wastewater treatment processes. This technology has the potential of reducing the infrastructure and operation costs of wastewater treatment by 25%, energy requirement by 30%, and space requirement by 75%. The nutrient removal mechanisms of aerobic granules are slightly different from that of the activated sludge. For instance, unlike activated sludge process, according to some reports, as high as 70% of the total phosphorus removed by aerobic granules were attributed to precipitation within the granules. Similarly, aerobic granule-based technology reduces the total amount of sludge produced during wastewater treatment. However, the reason behind this observation is unknown and it needs further explanations based on carbon and nitrogen removal mechanisms. Thus, as a part of the present review, a set of new hypotheses have been proposed to explain the peculiar nutrient removal mechanisms of the aerobic granules.     

Quantification of diatoms in biofilms: Standardisation of methods

Abstract

Benthic diatoms, which often dominate marine biofilms are mostly pennate along with a few centric species that have an attached mode of life. Even though the range of diatoms in biofilms is diverse, their ecology is poorly understood because of the difficulty in sampling and enumeration. Scraping or brushing are the traditional methods used for removal of diatoms from biofilms developed on solid substrata. The method of removal is the most critical step in enumerating the biofilm diatom community structure. In this study, a nylon brush and ceramic scraper were used as tools for the removal of diatoms from 1 – 4-day-old biofilms developed on fibreglass coupons and glass microscope slides. Standardisation of methods showed that the sample volume used in the analyses had the least influence on the quantification, whereas the method of removal was critical. The nylon brush was more efficient at recovering diatoms compared to a ceramic scraper. Direct microscopic enumeration of the community in the case of glass slides indicated that scraping resulted in between 30–50% underestimation. Heterogeneity in diatom community structure between replicate samples is one possible reason for such underestimation.     

Quantification of diatoms in biofilms: standardisation of methods

Benthic diatoms, which often dominate marine biofilms are mostly pennate along with a few centric species that have an attached mode of life. Even though the range of diatoms in biofilms is diverse, their ecology is poorly understood because of the difficulty in sampling and enumeration. Scraping or brushing are the traditional methods used for removal of diatoms from biofilms developed on solid substrata. The method of removal is the most critical step in enumerating the biofilm diatom community structure. In this study, a nylon brush and ceramic scraper were used as tools for the removal of diatoms from 1 - 4-day-old biofilms developed on fibreglass coupons and glass microscope slides. Standardisation of methods showed that the sample volume used in the analyses had the least influence on the quantification, whereas the method of removal was critical. The nylon brush was more efficient at recovering diatoms compared to a ceramic scraper. Direct microscopic enumeration of the community in the case of glass slides indicated that scraping resulted in between 30-50% underestimation. Heterogeneity in diatom community structure between replicate samples is one possible reason for such underestimation.     

Are removal experiments effective tools for assessing plant community resistance and recovery from invasion?

Removal experiments are useful tools for assessing two important aspects of plant community invasion: (1) resistance to invasion and (2) recovery after invasive species removal. We discuss the potential of such experiments based on a brief systematic review of the literature on community resistance, as measured by invasibility after removal of resident species (reduction of taxonomic/functional richness), and on community recovery, as measured by resident community response after invasive species removal. We found 62 research articles, most of them related to invasive species removal. Few studies used removals to test biotic resistance, despite the importance of resident removals for identifying community components that play key roles in the often‐controversial invasion resistance hypotheses. Furthermore, appropriate experimental controls were rarely used, which would allow separation of the effect of local species extinction from that of disturbance. We hope this review stimulates plant ecologists to adopt removal experiments for studying invasion processes.     

Removing interactions,rather than species,casts doubt on the high robustness of pollination networks

In the last 15 years, a complex networks perspective has been increasingly used in the robustness assessment of ecological systems. It is therefore crucial to assess the reliability of such tools. Based on the traditional simulation of node (species) removal, mutualistic pollination networks are considered to be relatively robust because of their 1) truncated power‐law degree distribution, 2) redundancy in the number of pollinators per plant and 3) nested interaction pattern. However, species removal is only one of several possible approaches to network robustness assessment. Empirical evidence suggests a decline in abundance prior to the extinction of interacting species, arguing in favour of an interaction removal‐based approach (i.e. interaction disruption), as opposed to traditional species removal. For simulated networks, these two approaches yield radically different conclusions, but no tests are currently available for empirical mutualistic networks. This study compared this new robustness evaluation approach based on interaction extinction versus the traditional species removal approach for 12 alpine and subalpine pollination networks. In comparison with species removal, interaction removal produced higher robustness in the worst‐case extinction scenario but lower robustness in the best‐case extinction scenario. Our results indicate that: 1) these two approaches yield very different conclusions and 2) existing assessments of ecological network robustness could be overly optimistic, at least those based on a disturbance affecting species at random or beginning with the least connected species. Therefore, further empirical study of plant–pollinator interactions in disturbed ecosystems is imperative to understand how pollination networks are disassembled.     

Methods for detection and visualization of intracellular polymers stored by polyphosphate-accumulating microorganisms

Polyphosphate-accumulating microorganisms (PAOs) are important in enhanced biological phosphorus (P) removal. Considerable effort has been devoted to understanding the biochemical nature of enhanced biological phosphorus removal (EBPR) and it has been shown that intracellular polymer storage plays an important role in PAO's metabolism. The storage capacity of PAOs gives them a competitive advantage over other microorganisms present that are not able to accumulate internal reserves. Intracellular polymers stored by PAOs include polyphosphate (poly-P), polyhydroxyalkanoates (PHAs) and glycogen. Staining procedures for qualitative visualization of polymers by optical microscopy and combinations of these procedures with molecular tools for in situ identification are described here. The strengths and weaknesses of widely used polymer quantification methods that require destruction of samples, are also discussed. Finally, the potential of in vivo nuclear magnetic resonance (NMR) spectroscopy for on-line measurement of intracellular reserves is reported.     

Microfluidics for cryopreservation

Cryopreservation has utility in clinical and scientific research but implementation is highly complex and includes labor-intensive cell-specific protocols for the addition/removal of cryoprotective agents and freeze-thaw cycles. Microfluidic platforms can revolutionize cryopreservation by providing new tools to manipulate and screen cells at micro/nano scales, which are presently difficult or impossible with conventional bulk approaches. This review describes applications of microfluidic tools in cell manipulation, cryoprotective agent exposure, programmed freezing/thawing, vitrification, and in situ assessment in cryopreservation, and discusses achievements and challenges, providing perspectives for future development.     

Current strategies for the use of affinity tags and tag removal for the purification of recombinant proteins

Affinity tags are highly efficient tools for protein purification. They allow the purification of virtually any protein without any prior knowledge of its biochemical properties. The use of affinity tags has therefore become widespread in several areas of research e.g., high throughput expression studies aimed at finding a biological function to large numbers of yet uncharacterized proteins. In some cases, the presence of the affinity tag in the recombinant protein is unwanted or may represent a disadvantage for the projected application of the protein, like for clinical use. Therefore, an increasing number of approaches are available at present that are designed for the removal of the affinity tag from the recombinant protein. Most of these methods employ recombinant endoproteases that recognize a specific sequence. These process enzymes can subsequently be removed from the process by affinity purification, since they also include a tag. Here, a survey of the most common affinity tags and the current methods for tag removal is presented, with special emphasis on the removal of N-terminal histidine tags using TAGZyme, a system based on exopeptidase cleavage. In the quest to reduce the significant costs associated with protein purification at large scale, relevant aspects involved in the development of downstream processes for pharmaceutical protein production that incorporate a tag removal step are also discussed. A comparison of the yield of standard vs. affinity purification together with an example of tag removal using TAGZyme is also included.     

Rat mitochondrion-neuron focused microarray (rMNChip) and bioinformatics tools for rapid identification of differential pathways in brain tissues

Mitochondrial function is of particular importance in brain because of its high demand for energy (ATP) and efficient removal of reactive oxygen species (ROS). We developed rat mitochondrion-neuron focused microarray (rMNChip) and integrated bioinformatics tools for rapid identification of differential pathways in brain tissues. rMNChip contains 1,500 genes involved in mitochondrial functions, stress response, circadian rhythms and signal transduction. The bioinformatics tool includes an algorithm for computing of differentially expressed genes, and a database for straightforward and intuitive interpretation for microarray results. Our application of these tools to RNA samples derived from rat frontal cortex (FC), hippocampus (HC) and hypothalamus (HT) led to the identification of differentially-expressed signal-transduction-bioenergenesis and neurotransmitter-synthesis pathways with a dominant number of genes (FC/HC = 55/6; FC/HT = 55/4) having significantly (p<0.05, FDR<10.70%) higher (≥1.25 fold) RNA levels in the frontal cortex than the others, strongly suggesting active generation of ATP and neurotransmitters and efficient removal of ROS. Thus, these tools for rapid and efficient identification of differential pathways in brain regions will greatly facilitate our systems-biological study and understanding of molecular mechanisms underlying complex and multifactorial neurodegenerative diseases.     

The pulsed water jet for selective removal of bone cement during revision arthroplasty]

Conventional tools used in prosthetic revision surgery have a limited range of action within the narrow cement mantle. Water jet cutting technology permits tiny and precisely controlled cuts, and may therefore be an alternative method of bone cement removal. Our study compares the cutting performance on bone cement (PMMA) and bone of a pulsed water jet and a continuous water jet. The aim of the study was to establish whether selective removal of PMMA is possible. 55 bone specimens (bovine femora) and 32 specimens of PMMA were cut with a continuous and a pulsed water jet at different pressures (40 MPa, 60 MPa) and pulse frequencies (0Hz, 50Hz, 250Hz). To ensure comparability of the results, the depths of cut were related to the hydraulic power of that part of the jet actually impinging on the material. While for PMMA the power-related depth of cut increased significantly with the pulse frequency, this did not apply to bone. The cuts produced in bone were sharp-edged. Since PMMA is more brittle than bone, the water jet caused cracks that enlarged further until particles of bone broke away. Although selective removal of PMMA without doing damage to the bone was not possible at the investigated settings of the jet parameters, the results do show that a pulsed water jet can cut bone cement much more effectively than bone. This is an important advantage over conventional non-selective tools for the removal of bone cement.     

Removing redundancy in SWISS-PROT and TrEMBL

SUMMARY: One of the distinguishing criteria of the SWISS-PROT protein sequence data bank is minimal redundancy. The introduction of TrEMBL as a supplementary database ensured the comprehensiveness of SWISS-PROT and TrEMBL but introduced some degree of redundancy. We developed a strategy to identify the redundancy present within and between SWISS-PROT and TrEMBL and its subsequent removal. AVAILABILITY: The tools mentioned in this paper are available on request.     

Application of rRNA-targeted oligonucleotide probes in biotechnology

Ribosomal RNA-targeted oligonucleotide probes have become valuable tools for the detection of microorganisms involved in important biotechnological processes. Microorganisms which are of major importance for processes such as wastewater treatment, microbial leaching or methane production can be detected and quantified in situ within a complex microbial community. For certain processes, such as nitrification or biological phosphate removal, new microorganisms have become the focus of interest and have led to an improved understanding of these bioremediation techniques. Hybridization techniques have become fast and reliable alternatives to conventional cultivation techniques in the food industry as a control method for starter cultures for fermentation processes or product control. Recent analytical tools such as flow cytometry and digital image processing have improved the efficiency of these techniques. This review is intended to present a summary of methodological aspects of rRNA-based hybridization techniques and their application in biotechnology.     

合成生物学技术在环境保护中的应用

合成生物学是一个基于生物学和工程学原理的科学领域,其目的是重新设计和重组微生物,以优化或创建具有增强功能的新生物系统。该领域利用分子工具、系统生物学和遗传框架的重编程,从而构建合成途径以获得具有替代功能的微生物。传统上,合成生物学方法通常旨在开发具有成本效益的微生物细胞工厂进而从可再生资源中生产化学物质。然而,近年来合成生物学技术开始在环境保护中发挥着更直接的作用。本综述介绍了基因工程中的合成生物学工具,讨论了基于基因工程的微生物修复策略,强调了合成生物学技术可以通过响应特定污染物进行生物修复来保护环境。其中,规律间隔成簇短回文重复序列(Clustered Regularly Interspersed Short Palindromic Repeats, CRISPR)技术在基因工程细菌和古细菌的生物修复中得到了广泛应用,生物修复领域也出现了很多新的先进技术,包括生物膜工程、人工微生物群落的构建、基因驱动、酶和蛋白质工程等。有了这些新的技术和工具,生物修复将成为当今最好和最有效的污染物去除方式之一。     

The substrate specificity of Metarhizium anisopliae and Bos taurus carboxypeptidases A: insights into their use as tools for the removal of affinity tags

Carboxypeptidases may serve as tools for removal of C-terminal affinity tags. In the present study, we describe the expression and purification of an A-type carboxypeptidase from the fungal pathogen Metarhizium anisopliae (MeCPA) that has been genetically engineered to facilitate the removal of polyhistidine tags from the C-termini of recombinant proteins. A complete, systematic analysis of the specificity of MeCPA in comparison with that of bovine carboxypeptidase A (BoCPA) was carried out. Our results indicate that the specificity of the two enzymes is similar but not identical. Histidine residues are removed more efficiently by MeCPA. The very inefficient digestion of peptides with C-terminal lysine or arginine residues, along with the complete inability of the enzyme to remove a C-terminal proline, suggests a strategy for designing C-terminal affinity tags that can be trimmed by MeCPA (or BoCPA) to produce a digestion product with a homogeneous endpoint.     

Species-specific visitation and removal of baits for delivery of pharmaceuticals to feral swine

Within the domestic swine industry there is growing trepidation about the role feral swine (Sus scrofa) play in the maintenance and transmission of important swine diseases. Innovative disease management tools for feral swine are needed. We used field trials conducted in southern Texas from February to March 2006 to compare species-specific visitation and removal rates of fish-flavored and vegetable-flavored baits with and without commercially available raccoon (Procyon lotor) repellent (trial 1) and removal rates of baits deployed in a systematic and cluster arrangement (trial 2). During trial 1, 1) cumulative bait removal rates after four nights ranged from 93% to 98%; 2) bait removal rates by feral swine, raccoons, and collared peccaries (Pecari tajacu) did not differ by treatment; and 3) coyotes (Canis latrans) removed more fish-flavored baits without raccoon repellent and white-tailed deer removed more vegetable-flavored baits without raccoon repellent than expected. During trial 2, feral swine removed fish-flavored baits distributed in a cluster arrangement (eight baits within 5 m2) at a rate greater than expected. Our observed bait removal rates illustrate bait attractiveness to feral swine. However, the diverse assemblage of omnivores in the United States compared with Australia where the baits were manufactured adds complexity to the development of a feral swine-specific baiting system for pharmaceutical delivery.     

Combining strains of lactic acid bacteria may reduce their toxin and heavy metal removal efficiency from aqueous solution

Aims: The primary objective of this study was to compare the removal of cadmium, lead, aflatoxin B₁ and microcystin‐LR from aqueous solution by Lactobacillus rhamnosus GG, L. rhamnosus LC705, Propionibacterium freudenreichii shermanii JS and Bifidobacterium breve Bbi99/E8, separately and in combination. Methods and Results: The removal of toxins and heavy metals was assessed in batch experiments. The removal of all compounds was observed to be strain specific. The removal of lead by a combination of all the strains used was observed to be lower than could be predicted from the removal by single strains (P < 0·05). A similar trend was also observed with the other compounds studied. Conclusions: The results show that the toxin‐removal capacity of a combination of strains of lactic acid bacteria is not the sum of their individual capacities. Therefore, pure single strains should be used when the goal is to remove single compounds. The use of combinations of strains may be beneficial when several compounds are removed together. This needs to be studied in future experiments. Significance and Impact of the Study: Lactic acid bacteria have been identified as potent tools for the decontamination of heavy metals, cyanotoxins and mycotoxins. The results of this study should be considered when selecting combinations of bacteria for the simultaneous removal of several toxic compounds.