Mapping the moral boundaries of biological engineering

The following essay was written by a sophomore undergraduate student majoring in Bioengineering at the University of Maryland, Mr. Zachary Russ. Mr. Russ was one of 174 students who submitted a 1000–1200 word essay to the 4th Annual Bioethics Contest sponsored by the Institute of Biological Engineering (IBE). A group of professionals in Biological Engineering assessed and ranked the essays in a blinded process. Five semi-finalists were invited to present their essays at a session at the annual meeting of IBE in Santa Clara, CA on March 21, 2009. Five judges scored all the presentation at the annual meeting and selected Mr. Russ's contribution as the overall winner (1st Place).     

Synthetic biology: enormous possibility,exaggerated perils

The following essay was written by a freshman undergraduate student majoring in Bioengineering at the University of Maryland, Mr. Zachary Russ. Mr. Russ was one of 94 students who submitted a 1000 to 1200 word essay to the 3rd Annual Bioethics Essay Contest sponsored by the Institute of Biological Engineering (IBE). A group of professionals in Biological Engineering assessed and ranked the essays in a blinded process. Five semi-finalists were invited to present their essays at a session at the annual meeting of IBE in Chapel Hill, NC on March 8, 2008. Five judges scored the presentations at the annual meeting and selected Mr. Russ's contribution as the overall winner (1st Place). Below is his essay.     

Grand challenges for biological engineering

Biological engineering will play a significant role in solving many of the world's problems in medicine, agriculture, and the environment. Recently the U.S. National Academy of Engineering (NAE) released a document "Grand Challenges in Engineering," covering broad realms of human concern from sustainability, health, vulnerability and the joy of living. Biological engineers, having tools and techniques at the interface between living and non-living entities, will play a prominent role in forging a better future. The 2010 Institute of Biological Engineering (IBE) conference in Cambridge, MA, USA will address, in part, the roles of biological engineering in solving the challenges presented by the NAE. This letter presents a brief outline of how biological engineers are working to solve these large scale and integrated problems of our society.     

In-vitro evaluation of Polylactic acid (PLA) manufactured by fused deposition modeling

October 10th, 2016 marked the 9th anniversary for the Journal of Biological Engineering (JBE), the official journal of Institute of Biological Engineering (IBE), published by BioMed Central. We are entering into the 10th year of its exciting and productive history. In this editorial, a brief history of JBE is summarized, along with a series of analyses on average number of citations, breakdown of topical subjects, geographical representations and so forth for all published articles in JBE. Future prospects and new directions of JBE are also described in this editorial.     

Partitioning the effects of isolation by distance,environment, and physical barriers on genomic divergence between parapatric threespine stickleback

Genetic divergence between populations is shaped by a combination of drift, migration, and selection, yielding patterns of isolation‐by‐distance (IBD) and isolation‐by‐environment (IBE). Unfortunately, IBD and IBE may be confounded when comparing divergence across habitat boundaries. For instance, parapatric lake and stream threespine stickleback (Gasterosteus aculeatus) may have diverged due to selection against migrants (IBE), or mere spatial separation (IBD). To quantitatively partition the strength of IBE and IBD, we used recently developed population genetic software (BEDASSLE) to analyze partial genomic data from three lake‐stream clines on Vancouver Island. We find support for IBD within each of three outlet streams (unlike prior studies of lake‐stream stickleback). In addition, we find evidence for IBE (controlling for geographic distance): the genetic effect of habitat is equivalent to geographic separation of ～1.9 km of IBD. Remarkably, of our three lake‐stream pairs, IBE is strongest where migration between habitats is easiest. Such microgeographic genetic divergence would require exceptionally strong divergent selection, which multiple experiments have failed to detect. Instead, we propose that nonrandom dispersal (e.g., habitat choice) contributes to IBE. Supporting this conclusion, we show that the few migrants between habitats are a nonrandom subset of the phenotype distribution of the source population.     

Characterization of IBE 2254 Binding to Alpha - Adrenergic Receptors on Intact DDT Smooth Muscle Cells: Comparison with Membrane1 Binding and Correlation with Phosphoinositides Breakdown

Abstract

The binding of the antagonist IBE 2254 (IBE) to α -adrenergic receptors was characterized on intact DDT smooth muscle cells. IBE binding was rapid, reversible, stable and saturable: Bmax = 113000±13000 recetors/cell, K = 110±13 pM (n = 25). Saturation and competition experiments analysed by non linear curve fitting indicated a single population of binding sites with a pharmacological profile typical for α-adrenergic receptors. Antagonists competed for IBE binding sites in the following order: prazosin > phentolamine = phenoxybenzamine > yohimbine. The rank order for agonists was clonidine > epinephrine > norepinephrine > phenylephrine. There was a significant correlation between IBE binding to intact cells, DDT₁ membranes and rat cortex membranes. Neither agonists nor antagonists showed noticeable changes in their affinity for IBE binding on either system. There was also a good correlation between IBE binding and breakdown of phosphoinositides (PI) measured in intact cells.     

Change is necessary in a biological engineering curriculum

Success of a Biological Engineering undergraduate educational program can be measured in a number of ways, but however it is measured, a presently successful program can translate into an unsuccessful program if it cannot adjust to different conditions posed by technical advances, student characteristics, and academic pressures. Described in this paper is a Biological Engineering curriculum that has changed significantly since its transformation from Agricultural Engineering in 1993. As a result, student numbers have continued to climb, specific objectives have emerged, and unique courses have been developed. The Biological Resources Engineering program has evolved into a program that emphasizes breadth, fundamentals, communications skills, diversity, and practical engineering judgment.     

Environmental gradients predict the genetic population structure of a coral reef fish in the Red Sea

The relatively recent fields of terrestrial landscape and marine seascape genetics seek to identify the influence of biophysical habitat features on the spatial genetic structure of populations or individuals. Over the last few years, there has been accumulating evidence for the effect of environmental heterogeneity on patterns of gene flow and connectivity in marine systems. Here, we investigate the population genetic patterns of an anemonefish, Amphiprion bicinctus, along the Saudi Arabian coast of the Red Sea. We collected nearly one thousand samples from 19 locations, spanning approximately 1500 km, and genotyped them at 38 microsatellite loci. Patterns of gene flow appeared to follow a stepping‐stone model along the northern and central Red Sea, which was disrupted by a distinct genetic break at a latitude of approximately 19°N. The Red Sea is characterized by pronounced environmental gradients along its axis, roughly separating the northern and central from the southern basin. Using mean chlorophyll‐a concentrations as a proxy for this gradient, we ran tests of isolation by distance (IBD, R² = 0.52) and isolation by environment (IBE, R² = 0.64), as well as combined models using partial Mantel tests and multiple matrix regression with randomization (MMRR). We found that genetic structure across our sampling sites may be best explained by a combined model of IBD and IBE (Mantel: R² = 0.71, MMRR: R² = 0.86). Our results highlight the potential key role of environmental patchiness in shaping patterns of gene flow in species with pelagic larval dispersal. We support growing calls for the integration of biophysical habitat characteristics into future studies of population genetic structure.     

Isolation by environment in White‐breasted Nuthatches (Sitta carolinensis) of the Madrean Archipelago sky islands: a landscape genomics approach

Understanding landscape processes driving patterns of population genetic differentiation and diversity has been a long‐standing focus of ecology and evolutionary biology. Gene flow may be reduced by historical, ecological or geographic factors, resulting in patterns of isolation by distance (IBD) or isolation by environment (IBE). Although IBE has been found in many natural systems, most studies investigating patterns of IBD and IBE in nature have used anonymous neutral genetic markers, precluding inference of selection mechanisms or identification of genes potentially under selection. Using landscape genomics, the simultaneous study of genomic and ecological landscapes, we investigated the processes driving population genetic patterns of White‐breasted Nuthatches (Sitta carolinensis) in sky islands (montane forest habitat islands) of the Madrean Archipelago. Using more than 4000 single nucleotide polymorphisms and multiple tests to investigate the relationship between genetic differentiation and geographic or ecological distance, we identified IBE, and a lack of IBD, among sky island populations of S. carolinensis. Using three tests to identify selection, we found 79 loci putatively under selection; of these, seven matched CDS regions in the Zebra Finch. The loci under selection were highly associated with climate extremes (maximum temperature of warmest month and minimum precipitation of driest month). These results provide evidence for IBE – disentangled from IBD – in sky island vertebrates and identify potential adaptive genetic variation.     

Ultrastructure of the compound eye and first optic neuropile of the photoreceptor mutant ora JK84 of Drosophila

Summary The developmental mutant of Drosophila (ora ^JK84) is characterized by nonfunctional photoreceptor cells (R1–6), while the R7/R8 cells are normal. A fundamental question is: Does the near absence of photosensitive membranes inhibit development of the Rl-6 axons and their synapses at the other end of the cell? The retina and first optic neuropile (lamina ganglionaris) were examined with freeze-fracture technique and high voltage electron microscopy. R1–6 have reduced rhabdomere caps; rhabdomeric microvilli have about 50% of the normal diameter and 20% of the normal length. Affected cells exhibit prominent vacuoles which appear to communicate with some highly convoluted microvillar membranes. Almost no P-face particles (putative rhodopsin molecules) are present in the R1–6 rhabdomeres, and particle densities are lower in R7 than previously reported. Near the rhabdomere caps, microvilli of R1–6 are fairly normal, but at more proximal levels they are greatly diminished in length and changed in orientation, while at still more proximal levels they are lost. R1–6, R7, and R8 axons from each ommatidium are bundled into normal pseudocartridges beneath the basement membrane. No abnormalities are found in the lamina ganglionaris, and all synaptic associations as well as the presumed virgin synapses (of R1–6) appear normal. No glial anomalies are present, and R7/R8 axons project through the lamina in the usual fashion. These fine structural findings are correlated with known electrophysiological, biochemical, and behavioral correlates of both sets of photoreceptors (R1–6, and R7/R8).This study was supported substantially by the UW-HVEM Laboratory, in addition to a Faculty Development Award, a UMC Biomedical Research Support Grant N.I.H. RR07053 to W.S.S., and a Hatch Grant, Project 2100 to S.D.C. Freeze fracture was done at the Wisconsin Regional Primate Research Center, N.I.H. Grant RR00167. We thank Professor Hans Ris, Dr. J. Pawley, Dr. D. Neuberger, and Ms. M. Bushlow, HVEM Laboratory, Dept. of Zoology, UW. We also thank Mrs. K. Srivastava, Mr. M.B. Garment, Mr. G. Gaard, and Mr. D. Liu for technical assistance.     

Relative importance of isolation-by-environment and other determinants of gene flow in an alpine amphibian

A pattern of population structure called isolation-by-environment (IBE) evolves when gene flow connecting populations in different habitats is lower than expected. Although IBE is widespread, there is limited information on its magnitude compared with other factors influencing gene flow. We estimated the relative importance of IBE in the frog Rana temporaria in the Swiss Alps, a geographic context in which IBE should be relatively pronounced. The environmental factor potentially causing IBE was the length of the growing season, which is highly correlated with elevation. A sample of 992 individuals from 82 breeding sites were genotyped at 1827 single-nucleotide polymorphism markers; gene flow was estimated in four ways related to F_ST, genetic distance, allele sharing, and distance on a population graph. Gravity modeling and random forest regression evaluated the importance of six at-site covariates, 10 between-site covariates, and geographic distance. There was broad agreement among analysis methods and measures of gene flow: isolation-by-distance (IBD) and habitat quality between sites were of highest importance, the elevation and ruggedness of the dispersal path were about half as important, and IBE was about 10–20% as important as IBD. These results combine with other evidence to suggest that population divergence across elevational gradients is underway in amphibians.     

Detection of factors of differentiation in human malignant melanoma

Factors of differentiation (FD) have been detected and isolated from human melanomas cloned in nude mice as well as from amphibian embryos from neurula--early tail bud stage. It has been shown that each source contains two factors of differentiation--mesodermalizing (MF) and melanogenic (MgF). Biological activity of MF has been determined by its capacity to initiate in early embryonic multipotent cells the appearance of various cell types, normally arising from mesoderm. Biological activity of MgF have been determined by its capacity to initiate melanogenesis both in epithelial cells and in dermal melanophores of clawed toad. It has been shown that both factors, isolated from both sources are heterogeneous by their molecular weights. Mr values determined for MgF, isolated from both sources, are nearly identical whereas Mr values of MF from sources coincide partially. Resemblance of FD detected in remote representatives of animal kingdom suggest the high evolutionary conservatism of factors, which switch on cell differentiation.     

试栽羊肚菌分子系统分析

[目的]为了弄清陕西汉中试栽羊肚菌的种类归属。[方法]收集到汉中地区试栽羊肚菌子实体19个样品,采用CTAB法提取其基因组DNA,使用通用引物PCR扩增5个基因序列(ITS、LSU、EF1-α、RPB1和RPB2)保守区片段,用1. 0%的琼脂糖凝胶电泳对PCR产物进行检测,并对PCR产物送样测序。依据测序结果构建系统发育树,结合系统发育树进行物种归属鉴定。[结果]获取了所有样品的5个基因序列保守区片段,通过测序比对19个样品5个基因序列保守区片段并进行序列联合,对总长度3 025 bp的保守区序列分析并构建系统发育树,依据系统发育树鉴定出汉中试栽羊肚菌分别为六妹羊肚菌(Morchella sextelata)、梯棱羊肚菌(M. importuna)、隐形羊肚菌(M. cryptica)和北方羊肚菌(M. septentrionalis)。[结论]采用多基因联合分析法弄清楚汉中试栽羊肚菌的种类归属。     

Growth and tissue formation from single geranium cells from virus-infected geraniums

Summary Single geranium (Pelargonium hortorum, Bailey) cells from callus isolated originally from stem tips of virus-infected plants were grown in microculture chambers in liquid Murashige and Skoog medium supplemented with 0.1 mg per liter of α-naphthalane acetic acid and 10.0 mg per liter of kinetin. Four of 1,000 of these single cells divided in the microculture chamber and produced colonies of 15 to 20 cells in 9 to 16 days. In all of the cases the plane of the first few cell division was at right angles to the long axis of the cells. Subsequently, one of the masses of cells obtained from a single cell, when transferred to solid Murashige and Skoog medium, established itself as a clone of callus tissue. Although the yield was low, the results were encouraging for the ultimate production of plants. These results suggested that, just as virus-free tobacco plants have been induced from single cell clones from certain tobacco species, virus-free single geranium cells may be useful to establish single cell clones from which pathogen-free geranium plants may be induced to differentiate. This work was supported by funds from USDA Hatch Project 981 and the NASA Institutional Grant. Published with the approval of the Director, Wisconsin Agricultural Experiment Station. The authors are indebted to Mr. E. H. Herrling and Mr. Steve Vicen for preparation of illustrations.     

Sample Size Determination for Individual Bioequivalence Inference

Statistical criterion for evaluation of individual bioequivalence (IBE) between generic and innovative products often involves a function of the second moments of normal distributions. Under replicated crossover designs, the aggregate criterion for IBE proposed by the guidance of the U.S. Food and Drug Administration (FDA) contains the squared mean difference, variance of subject-by-formulation interaction, and the difference in within-subject variances between the generic and innovative products. The upper confidence bound for the linearized form of the criterion derived by the modified large sample (MLS) method is proposed in the 2001 U.S. FDA guidance as a testing procedure for evaluation of IBE. Due to the complexity of the power function for the criterion based on the second moments, literature on sample size determination for the inference of IBE is scarce. Under the two-sequence and four-period crossover design, we derive the asymptotic distribution of the upper confidence bound of the linearized criterion. Hence the asymptotic power can be derived for sample size determination for evaluation of IBE. Results of numerical studies are reported. Discussion of sample size determination for evaluation of IBE based on the aggregate criterion of the second moments in practical applications is provided.     

Fibroblast growth factor-2 induces the activation of Src through Fes, which regulates focal adhesion disassembly

Cell migration is regulated by focal adhesion (FA) turnover. Fibroblast growth factor-2 (FGF-2) induces FA disassembly in the murine brain capillary endothelial cell line IBE, leading to FGF-2-directed chemotaxis. We previously showed that activation of Src and Fes by FGF-2 was involved in chemotaxis of IBE cells. In this study, we examined the interplay between Src and Fes. FGF-2 treatment decreased the number of FA in IBE cells, but not in cells expressing dominant-negative Fes (denoted KE5-15 cells). FGF-2 induced the activation of Src and subsequent binding to and phosphorylation of Cas in IBE cells, but not in KE5-15 cells. Focal adhesion kinase (FAK) activation and tyrosine phosphorylation by Src were also delayed in KE5-15 cells compared to parental cells. FGF-2 induced activation of Src within FA in IBE cells, but not in KE5-15 cells. Downregulation of Fes or FAK using small interfering RNA diminished Src activation by FGF-2 within FA. These findings suggest that activation of Fes by FGF-2 enhances FAK-dependent activation of Src within FA, promoting FGF-2-induced disassembly of focal adhesions.     

Hydrodynamics and mathematical modelling in a low HRT inverse fluidized-bed reactor for biological sulphate reduction

Bioprocess and Biosystems Engineering - Biological reduction of sulphate at low hydraulic retention time (HRT) is presented in this paper. A sulphidogenic inverse fluidized-bed bioreactor (IFBB)...     

Mitochondrial metabolic suppression and reactive oxygen species production in liver and skeletal muscle of hibernating thirteen-lined ground squirrels

During hibernation, animals cycle between periods of torpor, during which body temperature (T(b)) and metabolic rate (MR) are suppressed for days, and interbout euthermia (IBE), during which T(b) and MR return to resting levels for several hours. In this study, we measured respiration rates, membrane potentials, and reactive oxygen species (ROS) production of liver and skeletal muscle mitochondria isolated from ground squirrels (Ictidomys tridecemlineatus) during torpor and IBE to determine how mitochondrial metabolism is suppressed during torpor and how this suppression affects oxidative stress. In liver and skeletal muscle, state 3 respiration measured at 37°C with succinate was 70% and 30% lower, respectively, during torpor. In liver, this suppression was achieved largely via inhibition of substrate oxidation, likely at succinate dehydrogenase. In both tissues, respiration by torpid mitochondria further declined up to 88% when mitochondria were cooled to 10°C, close to torpid T(b). In liver, this passive thermal effect on respiration rate reflected reduced activity of all components of oxidative phosphorylation (substrate oxidation, phosphorylation, and proton leak). With glutamate + malate and succinate, mitochondrial free radical leak (FRL; proportion of electrons leading to ROS production) was higher in torpor than IBE, but only in liver. With succinate, higher FRL likely resulted from increased reduction state of complex III during torpor. With glutamate + malate, higher FRL resulted from active suppression of complex I ROS production during IBE, which may limit ROS production during arousal. In both tissues, ROS production and FRL declined with temperature, suggesting ROS production is also reduced during torpor by passive thermal effects.     

优化噬热栖热菌的遗传转化体系

[目的]优化噬热栖热菌Thermus thermophilus的转化体系。[方法]将质粒DNA的形态、浓度及转化时间作为变量设计噬热栖热菌T.thermophilus的转化体系,以通过直接双交换同源重组法获取Δpyr E突变体的概率为依据判定转化效率。[结果]在转化时间为2 h,使用3.0μg/m L线性质粒DNA,获取表观Δpyr E的概率为3.44×10^-5;而使用同样浓度的超螺旋质粒DNA,该概率可达1.03×10^-3;说明超螺旋质粒的转化效率高于线状质粒。质粒DNA的使用浓度及转化反应时间对转化效率亦有影响,但并非完全成正相关。使用浓度为15μg/m L超螺旋质粒DNA,在转化时间为3 h时,获取表观Δpyr E的概率达到最大值(1.36×10^-2);超过该阈值,转化效率降低。[结论]在T.thermophilus中,通过优化转化体系将基因无痕敲除突变体获取概率提高到10^-2。