Validating a low-cost,consumer force-measuring platform as an accessible alternative for measuring postural sway

The Zibrio SmartScale is a low-cost, portable force platform designed to perform an objective assessment of postural stability. The purpose of the present study was to validate the center of pressure (COP) measurements in the Zibrio SmartScale. Simultaneous COP data was collected by a Zibrio SmartScale and a laboratory-grade force platform (LFP) under the dynamic motion of an inverted pendulum device intended to mimic the sway of a standing human. The inverted pendulum was placed on the Zibrio SmartScale which was placed on the LFP. The pendulum was then displaced to angles of 3° and 5° in both the anterior-posterior (AP) and medial–lateral (ML) directions. The findings of this study show low mean average error (MAE) among the measures taken simultaneously upon the LFP and Zibrio SmartScale with no appreciable difference in error in either AP or ML COP directions. Averaged over repeated trials, the MAE did not surpass 0.5 mm. This represented 0.4% of the total range (±50 to 60 mm in 5° displacement trials) of simulated COP. The results of this study strongly indicate that the Zibrio SmartScale can perform adequately as a light-weight and low-cost alternative method of COP measurement in comparison to a traditional LFP.     

OrthoClusterDB: an online platform for synteny blocks

Background  

The recent availability of an expanding collection of genome sequences driven by technological advances has facilitated comparative genomics and in particular the identification of synteny among multiple genomes. However, the development of effective and easy-to-use methods for identifying such conserved gene clusters among multiple genomes–synteny blocks–as well as databases, which host synteny blocks from various groups of species (especially eukaryotes) and also allow users to run synteny-identification programs, lags behind.     

WebArray: an online platform for microarray data analysis

Background  

Many cutting-edge microarray analysis tools and algorithms, including commonly used limma and affy packages in Bioconductor, need sophisticated knowledge of mathematics, statistics and computer skills for implementation. Commercially available software can provide a user-friendly interface at considerable cost. To facilitate the use of these tools for microarray data analysis on an open platform we developed an online microarray data analysis platform, WebArray, for bench biologists to utilize these tools to explore data from single/dual color microarray experiments.     

Standardization of computer-assisted semen analysis using an e-learning application

Computer-assisted semen analysis (CASA) is primarily used to obtain accurate and objective kinetic sperm measurements. Additionally, AI centers use computer-assessed sperm concentration in the sample as a basis for calculating the number of insemination doses available from a given ejaculate. The reliability of data is often limited and results can vary even when the same CASA systems with identical settings are used. The objective of the present study was to develop a computer-based training module for standardized measurements with a CASA system and to evaluate its training effect on the quality of the assessment of sperm motility and concentration. A digital versatile disc (DVD) has been produced showing the standardization of sample preparation and analysis with the CASA system SpermVision™ version 3.0 (Minitube, Verona, WI, USA) in words, pictures, and videos, as well as the most probable sources of error. Eight test persons educated in spermatology, but with different levels of experience with the CASA system, prepared and assessed 10 aliquots from one prediluted bull ejaculate using the same CASA system and laboratory equipment before and after electronic learning (e-learning). After using the e-learning application, the coefficient of variation was reduced on average for the sperm concentration from 26.1% to 11.3% (P ≤ 0.01), and for motility from 5.8% to 3.1% (P ≤ 0.05). For five test persons, the difference in the coefficient of variation before and after use of the e-learning application was significant (P ≤ 0.05). Individual deviations of means from the group mean before e-learning were reduced compared with individual deviations from the group mean after e-learning. According to a survey, the e-learning application was highly accepted by users. In conclusion, e-learning presents an effective, efficient, and accepted tool for improvement of the precision of CASA measurements. This study provides a model for the standardization of other laboratory procedures using e-learning.     

PABS: an online platform to assist BAC-by-BAC sequencing projects

Genome sequencing projects are either based on whole genome shotgun (WGS) or on a BAC-by-BAC strategy. Although WGS is in most cases the preferred choice, sometimes the BAC-by-BAC approach may be better because it requires a much simpler assembly process. Furthermore, when the study is limited to specific regions of the genome, the WGS would require an unjustified effort, making the BAC-by-BAC the only feasible strategy. In this paper we describe an informatics pipeline called PABS (Platform Assisted BAC-by-BAC Sequencing) that we developed to provide a tool to optimize the BAC-by-BAC sequencing strategy. PABS has two main functions: (i) PABS-Select, to choose suitable overlapping clones; and (ii) PABS-Validate, to verify whether a BAC under analysis is actually overlapping the neighboring BAC.     

Podcasting as a tool to take conservation education online

Traditional forms of higher learning include teaching in the classroom on college campuses and in‐person adult‐focused public outreach events for non‐students. Online college degree programs and public outreach platforms have been steadily emerging, and the COVID‐19 pandemic has, at least temporarily, forced all related ecology and evolutionary biology programs to move to online delivery. Podcasting is a form of online mass communication that is rapidly gaining popularity and has the flexibility to be incorporated into the pedagogical toolbox for the online classroom and remote public outreach programming. Podcasting is also becoming more popular in the ecology and evolutionary biology field. Here, we describe the great potential of podcasting to transform the learning experience, present a case study of success from the United States, provide a table of podcast recommended by ecologist responding to a listserv, and provide a road map for adoption and utilization of podcasting for the future.     

Chimpanzee identification and social network construction through an online citizen science platform

Citizen science has grown rapidly in popularity in recent years due to its potential to educate and engage the public while providing a means to address a myriad of scientific questions. However, the rise in popularity of citizen science has also been accompanied by concerns about the quality of data emerging from citizen science research projects. We assessed data quality in the online citizen scientist platform Chimp&See, which hosts camera trap videos of chimpanzees (Pan troglodytes) and other species across Equatorial Africa. In particular, we compared detection and identification of individual chimpanzees by citizen scientists with that of experts with years of experience studying those chimpanzees. We found that citizen scientists typically detected the same number of individual chimpanzees as experts, but assigned far fewer identifications (IDs) to those individuals. Those IDs assigned, however, were nearly always in agreement with the IDs provided by experts. We applied the data sets of citizen scientists and experts by constructing social networks from each. We found that both social networks were relatively robust and shared a similar structure, as well as having positively correlated individual network positions. Our findings demonstrate that, although citizen scientists produced a smaller data set based on fewer confirmed IDs, the data strongly reflect expert classifications and can be used for meaningful assessments of group structure and dynamics. This approach expands opportunities for social research and conservation monitoring in great apes and many other individually identifiable species.     

Plant endophytes as a platform for discovery-based undergraduate science education

Project ownership is an essential but sometimes overlooked ingredient for a successful undergraduate research experience. We have embarked on an experiment in undergraduate education that targets isolation of microbes from rainforest plants and characterization of natural products as objectives for discovery-based undergraduate research.     

Quantifying an online wildlife trade using a web crawler

Biodiversity and Conservation - Legally protected plants are illegally traded through online sales platforms and orchids are a significant component of this wildlife trade. This study focused on...     

Biomolecule-embedded metal-organic frameworks as an innovative sensing platform

Technological advancements combined with materials research have led to the generation of enormous types of novel substrates and materials for use in various biological/medical, energy, and environmental applications. Lately, the embedding of biomolecules in novel and/or advanced materials (e.g., metal-organic frameworks (MOFs), nanoparticles, hydrogels, graphene, and their hybrid composites) has become a vital research area in the construction of an innovative platform for various applications including sensors (or biosensors), biofuel cells, and bioelectronic devices. Due to the intriguing properties of MOFs (e.g., framework architecture, topology, and optical properties), they have contributed considerably to recent progresses in enzymatic catalysis, antibody-antigen interactions, or many other related approaches. Here, we aim to describe the different strategies for the design and synthesis of diverse biomolecule-embedded MOFs for various sensing (e.g., optical, electrochemical, biological, and miscellaneous) techniques. Additionally, the benefits and future prospective of MOFs-based biomolecular immobilization as an innovative sensing platform are discussed along with the evaluation on their performance to seek for further development in this emerging research area.     

A fully online sensor-equipped,disposable multiphase microbioreactor as a screening platform for biotechnological applications

A new disposable, multiphase, microbioreactor (MBR; with a working volume of 550 μl) equipped with online sensors is presented for biotechnological screening research purposes owing to its high-throughput potential. Its design and fabrication, online sensor integration, and operation are described. During aerobic cultivation, sufficient oxygen supply is the most important factor that influences growth and product formation. The MBR is a microbubble column bioreactor (μBC), and the oxygen supply was realized by active pneumatic bubble aeration, ensuring sufficient volumetric liquid-phase mass transfer (k _L a) and proper homogenization of the cultivation broth. The μBC was equipped with miniaturized sensors for the pH, dissolved oxygen, optical density and glucose concentration that allowed real-time online monitoring of these process variables during cultivation. The challenge addressed here was the integration of sensors in the limited available space. The MBR was shown to be a suitable screening platform for the cultivation of biological systems. Batch cultivations of Saccharomyces cerevisiae were performed to observe the variation in the process variables over time and to show the robustness and operability of all the online sensors in the MBR.     

Global proteome discovery using an online three-dimensional LC-MS/MS

We have developed a proteomics technology featuring on-line three-dimensional liquid chromatography coupled to tandem mass spectrometry (3D LC-MS/MS). Using 3D LC-MS/MS, the yeast-soluble, urea-solubilized peripheral membrane and SDS-solubilized membrane protein samples collectively yielded 3019 unique yeast protein identifications with an average of 5.5 peptides per protein from the 6300-gene Saccharomyces Genome Database searched with SEQUEST. A single run of the urea-solubilized sample yielded 2255 unique protein identifications, suggesting high peak capacity and resolving power of 3D LC-MS/MS. After precipitation of SDS from the digested membrane protein sample, 3D LC-MS/MS allowed the analysis of membrane proteins. Among 1221 proteins containing two or more predicted transmembrane domains, 495 such proteins were identified. The improved yeast proteome data allowed the mapping of many metabolic pathways and functional categories. The 3D LC-MS/MS technology provides a suitable tool for global proteome discovery.     

Au-nanoparticles as an electrochemical sensing platform for aptamer-thrombin interaction

A novel electrochemical method for the detection of bioaffinity interactions based on a gold-nanoparticles sensing platform and on the usage of stripping voltammetry technique was developed. The oxidation of gold surface (resulted in gold oxide formation) upon polarization served as a basis for analytical response. As a model, thrombin-thrombin binding aptamer couple was chosen. The aptamer was immobilized on a screen-printed electrode modified with gold-nanoparticles by avidin-biotin technology. Cathodic peak area was found proportional to thrombin quantity specifically adsorbed onto electrode surface. Sigmoid calibration curve as is typical for immunoassay was obtained, with thrombin detection limit of 10(-9)M. Linear range corresponds from 10(-8) to 10(-5)M thrombin concentration or 2 x 10(-14) to 2 x 10(-11)mol/electrode (R=0.996). Binding of thrombin to an aptamer has also been detected using the ferricyanide/ferrocyanide redox couple as electrochemical indicator.     

Metabolic engineering as an integrating platform for strain development

Integration of the analytical framework and experimental tools of metabolic engineering with emerging technologies such as DNA microarrays and directed evolution stands to dramatically improve the approaches by which strain improvement and biocatalyst design are pursued in the future. Progress in genomics and applied molecular biology, together with increasing emphasis on renewable resource utilization for chemical production, has advanced metabolic engineering to the forefront of biotechnological interest.     

Evolutionary remnants as widely accessible evidence for evolution: the structure of the argument for application to evolution education

Evolution education, in both schools and informal education, often focuses on natural selection and the fit of organisms through natural selection to their environment and way of life. Examples of evidence that evolution has occurred are therefore often limited to a modest number of classic but exotic cases, with little attention to how one might apply principles to more familiar organisms. Many of these classic examples are examples of adaptation; adaptation to local environments is, however, an outcome that could in principle also be explained by supernatural creation or design. A frequent result is the perception among the public is that examples of evolution are rare, and that the existence of well-adapted organisms may just as easily be explained metaphysically. We argue that among categories of evidence of evolution accessible to non-specialists in any environment, the most compelling evidence of common ancestry consists of remnants of evolutionary history evident in homologous features, particularly when those homologies are related to lack of fit of organisms to their way of life (“vestiges”) or to better fit that involves complicated combinations of parts usually assigned other functions (“contrivances”). Darwin emphasized the critical nature of this argument from imperfections, and it has been part of traditional catalogs of “evidence for evolution” for more than a century. Yet while remnants of history are widely used as a category of evidence for evolution, their utility in education of comparative anatomy to document body parts passed on through descent is underemphasized in evolution education at all levels. We explore the use of evolutionary remnants to document common ancestry and evidence for evolution, for application to evolution education.     

A fluorescence polarization assay using an engineered human respiratory syncytial virus F protein as a direct screening platform

Human respiratory syncytial virus (hRSV) typically affects newborns and young children. Even though it can cause severe and, in some cases, lifelong respiratory infections, there are currently no Food and Drug Administration (FDA)-approved therapeutics that control this virus. The hRSV F protein facilitates viral fusion, a critical extracellular event that can be targeted for therapeutic intervention by disrupting the assembly of a postfusion 6-helix bundle (6HB) within the hRSV F protein. Here we report the development of a fluorescence polarization (FP) assay using an engineered hRSV F protein 5-helix bundle (5HB). We generated the 5HB and validated its ability to form a 6HB in an FP assay. To test the potential of 5HB as a screening tool, we then investigated a series of truncated peptides derived from the “missing” sixth helix. Using this FP-based 5HB system, we have successfully demonstrated that short peptides can prevent 6HB formation and serve as potential hRSV fusion inhibitors. We anticipate that this new 5HB system will provide an effective tool to identify and study potential antivirals to control hRSV infection.