BioScience

Published by Oxford University Press (OUP)
Online ISSN: 1525-3244
Publications
Article
Red light initiates many important morphogenetic responses in plants through the mediation of the pigment, phytochrome. How phytochrome promotes photomorphogenesis is unknown. The evidence that photoactivated phytochrome initiates calcium fluxes in cells is reviewed and how these fluxes could regulate several known red-light induced effects in plants is discussed.
 
Article
Achieving trainee diversity in science, technology, engineering, and mathematics is rapidly becoming a challenge faced by many nations. Success in this area ensures the availability of a workforce capable of engaging in scientific practices that will promote increased production capacity and creativity and will preserve global scientific competitiveness. The near-term vision of achieving this goal is within reach and will capitalize on the growing numbers of underrepresented minority groups in the population. Although many nations have had remarkable histories as leaders in science and technology, few have simultaneously struggled with the challenge of meeting the educational and training needs of underrepresented groups. In this article, we share strategies for building the agency of the scientific community to achieve greater diversity by highlighting four key action areas: (1) aligning institutional culture and climate; (2) building interinstitutional partnerships; (3) building and sustaining critical mass; and (4) ensuring, rewarding, and maximizing faculty involvement.
 
Article
The impact of life on the atmosphere is examined through a discussion of the budgets of important atmospheric constituents and the processes that control their concentrations. Life profoundly influences oxygen and a number of minor atmospheric constituents, but many important gases, including those with the greatest effect on global climate, appear to be little altered by biological processes, at least in the steady state.
 
Article
There is a particularly urgent need to analyze population policy debates because of the serious nature of the disagreements that exist and the serious consequences either of choosing the wrong policies or of choosing none. The significant sources of agreement and disagreement about population policy are described and include a description of 3 major groups whose population policy recommendations vie for acceptance: crisis environmentalists family planners and developmental distributivists. These 3 groups represent distinct policy orientations and priorities. The crisis environmentalists take the view that rapid population growth has already produced a serious crisis for the human species and the planet earth. They all agree that resources needed for the survival of the human species are finite and will be depleted unless population is held at a level that establishes a favorable balance between numbers of people and available resources. Family planners like crisis environmentalists also speak of overpopulation at times but their focus more often is upon unwanted fertility or rapid population growth. They favor complete voluntarism in the form of government investment in free-standing birth control clinics to offer all the available methods of birth control to those who would not otherwise be able to afford them. This is in contrast to the crisis environmentalists who recommend coercive government policies. The developmental distributivists believe that certain kinds of improvements in socioeconomic conditions lead to lower birthrates as observed in the demographic transition experienced in Western countries. This group regards unfavorable socioeconomic conditions as major causes of large families and rapid population growth. They argue that the key to lowering fertility lies in the extensiveness of the distribution of benefits.
 
Article
Natural and synthetic estrogens are discussed with regard to their use as feed additives or as implanted pellets to increase the growth rate of ruminants. A system of evaluations is proposed to insure the safe use of estrogens as feed additives based on scientific principles and which will, after the necessary data are collected, provide a basis for making rational judgments. These principles should be applicable to other hormones which influence tumor formation. Relevant legislation controlling the use of feed additives are reviewed, as well as the results of earlier studies. The role of estrogens as carcinogens or cocarcinogens at high dosage levels is discussed and evidence that estrogens are not carcinogenic at all dosage levels is examined. Attention is also given to the available tests for determining the safety of hormonal residues, including suggested procedures for testing safe levels of the natural estrogens and alternative testing procedures for natural and synthetic estrogens.
 
Article
It is possible that growing public concern reflects an increasing desire by individuals to control their own lives (and deaths) and increasing unwillingness to accept unquestionably the physician's judgment. If they are to exercise their rights in a meaningful fashion, patients and families alike will have to educate themselves in advance about the complexities of medical technology and the problems which it can create for medical care. By the time they are actually faced with such decisions, they should know what sorts of alternatives they prefer. Should this happen, physicians in the future may find it necessary to treat the chronically ill patient less as a dependent for whom decisions have to be made and more as an equal. The new demand for greater patient autonomy also means that it is imperative to resolve some of the differences which now separate the perspective of the physician on these matters from that of the layman and the lawyer.
 
Article
Our minds are incarcerated by our words. The biological term symbiosis has been used in a way that obscures not only its literal meaning but also the phenomenon’s instrumental role in evolution. Biology textbooks define “symbiosis” anthropocentrically—as mutually helpful relationships or animal benefits, implying social contract or cost-benefit analysis by the partners. This definition is silly—symbiosis is a widespread biological phenomenon that preceded by eons the human world and the invention of money.
 
Article
This paper addresses the traditional concept of the levels of biological organization and presents an alternative, organism-centered scheme, depicting four types of biological relationships. The scheme emphasizes essential differences between the nature of the relationships subsumed under the concepts of community and ecosystem.
 
Article
There are hundreds of Biological Resource Centers (BRCs) around the world, holding many little-studied microorganism. The proportion of bacterial strains that is well represented in the sequence and literature databases may be as low as 1%. This body of unexplored diversity represents an untapped source of useful strains and derived products. However, a modicum of phenotypic data is available for almost all the bacterial strains held by BRCs around the world. It is at the phenotypic level that our knowledge of the well-studied strains of bacteria and the many yet-to-be studied strains intersects. This suggests we might leverage the phenotypic data from the data-poor bacteria with the omics data from the data-rich bacteria, using our knowledge of their evolutionary relationships, to map the metabolic networks of the little-known bacteria. This systems biology-based approach is a new way to explore the diversity harbored in BRCs.
 
Article
In treatises on evolution and related topics, conflicting views on fundamental issues raise serious problems. Such diverse views are especially puzzling to the nonbiologist who wishes to attain a fundamental knowledge of these topics but is stymied as to whose doctrines are to be utilized. A plea for help is thus in order.
 
Examples of shifts in the wavelength of maximum absorption (λ max , in nanometers) affected by amino acid interactions. The black, purple, blue, green, and red colors indicate various RH1, RH2, SWS1, SWS2, MWS, and LWS pigments. The arrows reflect the λ max shifts of visual pigments from different species and are named in order from top to bottom within each example. (a) The insertion (ins) of F86 in the SWS1 pigment of scabbardfish (Lepidopus fitchi) and deletions (del) of F86 in the SWS1 pigments of a vertebrate ancestor, the lampfish (Stenobrachius leucopsarus) and the bluefin killifish (Lucania goodei) (Tada et al. 2009). (b) S90C in the SWS1 pigments of the mouse (Mus musculus), the cow (Bos taurus), an avian ancestor, the pigeon (Columba livia), the frog (Xenopus laevis), and the chicken (Gallus gallus) and C90S in the SWS1 pigments of the budgerigar (Melopsittacus undulatus) and the zebra finch (Taeniopygia guttata). (c) T118A in the RH1 pigment of the cow and A118T in the SWS1 pigment of the budgerigar. (d) A292S in three ancestral, five bovine, and one tilapia (Oreochromis niloticus) RH1 pigments; in the SWS2 pigments of the bluefin killifish and the newt (Cynops pyrrhogaster); and in the LWS pigments of two ancestral M/LWS pigments and S292A in the RH1 pigments of the scabbardfish, the coelacanth (Latimeria chalumnae), the cichlid, the thornyhead (Sebastolobus altivelis), the viperfish (Chauliodus macouni), and the conger (Conger myriaster); in the RH2 pigment of the medaka (Oryzias latipes); in the SWS1 pigment of the human (Homo sapiens); and in the M/LWS pigments of the mouse and the dolphin (Tursiops truncatus) (Yokoyama 2008, Yokoyama et al. 2008a). (e) Single and multiple mutations in the RH1 pigment of the conger. (f) Single and multiple mutations in the SWS1 pigment of a frog ancestor (Takahashi and Yokoyama 2005). (g) G90S in two bovine RH1 pigments and S90G in bovine and human SWS1 pigments. (h) E113D in the SWS1 pigments of the frog and of its ancestor and E113D in two bovine RH1 pigments. See Yokoyama (2008) and the references therein. 
The composite maximum likelihood tree of 38 representative RH1 pigments in vertebrates. The black, blue, white, and red ovals indicate the experimentally determined deep-sea (wavelength of maximum absorption [λ max ] = 480-485 nanometers [nm]), intermediate (λ max = 490-495 nm), surface (λ max = 500-507 nm), and red-shifted (λ max = 526 nm) pigments, respectively, and the rectangles indicate λ max values estimated theoretically (Yokoyama et al. 2008b). The black, blue, and red branches show that no shift, blue shifts, and red shifts in λ max , respectively, occurred. Nine A292S substitutions are indicated by asterisks (*).
The absorption spectra of SWS1 pigments in (a) the pigeon, (b) the mouse, and (c) the human. Abbreviation: nm, nanometers. 
The hydrogen-bond network of bovine rhodopsin (pdb 1U19), connected by six amino acid sites and two nearby water molecules (W1 and W2).
Article
Natural selection has played an important role in establishing various phenotypes, but the molecular mechanisms of phenotypic adaptation are not well understood. The slow progress is a consequence of mutagenesis experiments in which present-day molecules were used and of the limited scope of statistical methods used to detect adaptive evolution. To fully appreciate phenotypic adaptation, the precise roles of adaptive mutations during phenotypic evolution must be elucidated through the engineering and manipulation of ancestral phenotypes. Experimental and quantum chemical analyses of dim-light vision reveal some surprising results and provide a foundation for a productive study of the adaptive evolution of various phenotypes.
 
Article
An important aspect of environmental control in a life-support system is the monitoring and regulation of atmospheric gases (Sager et al. 1988) at concentrations required for the maintenance of all life forms. It will be necessary to know the rates of CO2 use, oxygen evolution, and water flux through evapotranspiration by a crop stand under various environmental conditions, so that appropriate designs and control systems for maintaining mass balances of those gases can be achieved for a full range of environmental regimes. Mass budgets of gases will also enable evaluation of crop health by monitoring directly the rates of gas exchange and indirectly the rate of accumulation of dry matter, based on rates of carbon dioxide use. This article focuses on the unique capabilities of the NASA biomass production chamber for monitoring and evaluating gas exchange rates, with special emphasis on results with wheat and soybean, two candidate species identified by NASA for CELSS.
 
Article
This article represents an effort to examine the existing practices and the concepts which underlie them, and to indicate what can be done to help patients cope with dying without breaking the fundamental restrictions which our society justly places on the taking of lives.
 
Article
The cellular slime mold system has many features that make it a unique model system for the study of cellular differentiation. In recent years, genetics has played an increasingly important role in the development of the system. This paper reviews that progress.
 
Article
This paper summarizes the history and recent acceleration of progress in research on reproduction leading to improved means of contraception, in relation to worldwide funding. The authors list recommendations respecting the immediate need for a greatly expanded research effort to attain contraceptive means that are safe, effective, reversible, easily available, and widely acceptable for long-term use.
 
The morphology of vertebrate cone and rod photoreceptors. Each includes an inner segment and an outer segment, connected by a cilium. The inner segment contains the cell's biosynthetic machinery. Phototransduction takes place in the outer segment. In the rods, the outer segment contains free-floating membrane-bound disks. In the cones, the disks remain continuous with the plasma membrane. Source: Modified from Perkins and Fadool (2010) with permission from Elsevier.
(a) Photomicrograph of a method for electrical recording from an isolated primary cilium. A glass-coated bead is covered with a confluent layer of renal epithelial (IMCD-3) cells. A smooth arc (indicated by the arrow) has been drawn to represent the boundary between the bead and the cells. The primary cilium belonging to one cell is visible entering the tip of the recording micropipette. Cells are grown on beads to increase the visibility of the cilia. In a typical planar monolayer culture, the cilia cannot be resolved above the underlying cell layer. Another advantage of the procedure shown is that the bead is free floating. This allows the cilium to enter the recording pipette as suction is applied to the pipette. The scale bar represents 10 micrometers. Source: Reprinted with permission from Kleene and Kleene (2012). (b) A continuous 2-second recording of the current across the membrane of a renal primary cilium that was detached from the cell. The recording shows current fluctuations due to the opening and closing of a single membrane channel. The lower level of current (the dashed lines) is seen when the channel is closed, and a current 5.2 picoamperes (pA) greater is seen when the channel is open. The membrane potential was held at 0 millivolts. This channel was activated by applying 4-micromolar Ca 2+ to the cytoplasmic face of the membrane. Abbreviation: ms, milliseconds.  
(a) Wild type Paramecium cell with the FLAGepitope-tagged small-conductance calcium ion–activated potassium ion channel SK1a. The FLAG-tagged channel is visualized with an anti-FLAG primary and a red fluorescent secondary antibody. The green fluorescence of the cell body and spots in the cilia are from an antibody against the folate chemoreceptor and secondary antibody. Note the red cilia, which indicate that the SK1a channel localizes primarily to the cilia. (b) Wild type Paramecium cell with the PKD2 channel FLAG-epitope tagged. The red fluorescence indicates that this channel is present in cilia and also on the general cell surface. The green punctate fluorescence on the cell body is from the primary and secondary antibodies used to identify centrin, a protein known to be present in basal bodies at the base of the cilia. The scale bar indicates 10 micrometers. Source: Reprinted with permission from Valentine and colleagues (2012).  
Article
Cilia are highly conserved for their structure and also for their sensory functions. They serve as antennae for extracellular information. Whether the cilia are motile or not, they respond to environmental mechanical and chemical stimuli and send signals to the cell body. The information from extracellular stimuli is commonly converted to electrical signals through the repertoire of ion-conducting channels in the ciliary membrane, which results in changes in concentrations of ions, especially calcium ions, in the cilia. These changes, in turn, affect motility and the ability of the signaling pathways in the cilia and cell body to carry on the signal transduction. We review here the activities of ion channels in cilia in animals from protists to vertebrates.
 
Schematic of biphasic electric organ discharge production by a hypopomid electric fish of the genus Brachyhypopomus. The electric organ is composed of rows of electrocytes in series to sum voltages, and multiple series (three shown here) in parallel to sum currents. To create the first phase (P1), the innervated posterior face fires an action potential on every electrocyte, creating a headward current that makes the head positive relative to the tail. Next, the anterior faces of the posterior twothirds of the electrocytes discharge, creating a tailward current that makes the tail positive relative to the head (P2). 
Electric field vector plots of electric organ discharge (EOD) measured along the side of a female Brachyhypopomus beebei (a). The vector plots (b), drawn to scale, show the electric field vectors in the lateral plane measured at each of the points on the adjacent dotted line. Vectors are plotted at six time points in the EOD, numbered 1-6. Numbers to the left of each vector row correspond to the times marked on the accompanying EOD waveform. Intensity in each vector row is shown relative to the vertical scale bar. Spinal propagation of the discharge command from the brain appears in the initial strengthening of vectors at the anterior end of the fish (time point 1), whereupon more posterior areas become activated. The tail of the fish produces more intense electric fields than the trunk or head. Adapted from Stoddard and colleagues (1999). 
This collection of signals, a mix of synthesized waveforms and digitized electric organ discharges (EODs), shows the importance of symmetry around the zero ordinate value for suppressing low-frequency energy. On the left are synthetic signals and their counterparts from gymnotiform electric fish. On the right are the corresponding power spectra. The gray bars span 0-60 hertz (Hz), the spectral sensitivity of ampullary electroreceptors, which are used by predators to "eavesdrop" on the EODs of weakly electric fish. Those signals that show symmetry around zero in the voltage/time waveforms also show spectral suppression of energy in the range of ampullary electroreceptors. Continuous waveforms (a, e, f) have narrow spectra, in contrast to transient "pulse" waveforms (b-d, g), which have broad spectra. 
(a) Developmental series of electric organ discharges (EODs) of a Brachyhypopomus pinnicaudatus. EOD waveforms have been rescaled to equate the amplitude of the first phase. Age is shown as the number of days postfertilization. When the fish is very small, its EODs are monophasic (day 17), with maximal power in the spectral range of the ampullary electroreceptors (gray bar). As the fish grows, the electric organ produces an increasingly biphasic EOD waveform. By 110 days, energy in the spectral range of the ampullary electroreceptors has been suppressed by 15 decibels, rendering the young fish much less vulnerable to predators than it would have been had it retained the initial monophasic waveform. (b) EOD waveforms and spectra of male and female B. pinnicaudatus. At night, the second phase of the male's EOD is considerably extended, which increases spectral energy in the sensory range of the ampullary electroreceptors (gray bar). The female's EOD changes only slightly (not shown).
Article
Electric fish produce weak electric fields to image their world in darkness and to communicate with potential mates and rivals. Eavesdropping by electroreceptive predators exerts selective pressure on electric fish to shift their signals into less-detectable high-frequency spectral ranges. Hypopomid electric fish evolved a signal-cloaking strategy that reduces their detectability by predators in the lab (and thus presumably their risk of predation in the field). These fish produce broad-frequency electric fields close to the body, but the heterogeneous local fields merge over space to cancel the low-frequency spectrum at a distance. Mature males dynamically regulate this cloaking mechanism to enhance or suppress low-frequency energy. The mechanism underlying electric-field cloaking involves electrogenic cells that produce two independent action potentials. In a unique twist, these cells orient sodium and potassium currents in the same direction, potentially boosting their capabilities for current generation. Exploration of such evolutionary inventions could aid the design of biogenerators to power implantable medical devices, an ambition that would benefit from the complete genome sequence of a gymnotiform fish.
 
Article
The case of Karen Ann Quinlan has focused nationwide attention on the legal bounds of a decision to withdraw life-preserving care from a lingering patient. This comment on the lower court decision in the Quinlan case suggests that the judge was overly restrictive of the family's prerogatives.
 
Group selection experiments. (a) Choose units of selection with a variable phenotype (  ) from a common stock. Maintain parent populations (P) under identical environmental conditions. Select a fraction of each of the parent populations that express a phenotypic value at the upper end of the frequency distribution (for high line). The null line is a control that excludes the possibility of group selection. Random line units are selected randomly (S  r  ) as an additional control. We would usually predict no significant change in  of the null or random lines. Mix the selected microcosms to produce new populations (O 1  ). Repeat using the offspring populations as the new parents (O n ). (b) The response to selection is a statistically significant difference between the mean phenotype (  ) of the high and low lines, shown here as nonoverlapping confidence intervals. (c) The main distinction between individual and group selection experiments is the unit of selection, the definition of  , and the calculation of  . Groups of organisms form the unit of selection and  is a property of individual groups.  is a property of a group of groups. 
Artificial ecosystem selection experiments share some similarities with other more established microbiology techniques. Enrichment, direct plating, and artificial ecosystem selection all perform dilution of a diverse community, but there are crucial differences among them. The most critical differences are the rate of dilution events and the composition of the growth medium. Another technique commonly used to study diverse communities is long-term treatment. Treatment experiments can be performed in laboratory microcosms or in natural environments. An environmental parameter such as addition of fertilizers is varied across a replicate-block experimental design and the resident communities are allowed to adjust for a relatively long period (e.g., Chu et al. 2007). In in situ soil treatment experiments, the dilution rate is necessarily zero. 
Article
Artificial ecosystem selection is an experimental technique that treats microbial communities as though they were discrete units by applying selection on community-level properties. Highly diverse microbial communities associated with humans and other organisms can have significant impacts on the health of the host. It is difficult to find correlations between microbial community composition and community-associated diseases, in part because it may be impossible to define a universal and robust species concept for microbes. Microbial communities are composed of potentially thousands of unique populations that evolved in intimate contact, so it is appropriate in many situations to view the community as the unit of analysis. This perspective is supported by recent discoveries using metagenomics and pangenomics. Artificial ecosystem selection experiments can be costly, but they bring the logical rigor of biological model systems to the emerging field of microbial community analysis.
 
Article
Recently scientists have proposed that some, if not all, ancient glacial deposits are really impact deposits. The proposition that glaciation may not have occurred before the Cenozoic raises for reconsideration the surface temperature history of earth. The authors examine the information available and propose the following scenario. Just before the origin of life, the earth had a high carbon dioxide pressure-cooker atmosphere and soon after extreme thermophiles colonized the land, enhancing weathering rates, sequestering carbon dioxide into limestone deposits and cooling the Earth's surface. Subsequent cooling of the earth and enhancement of weathering was in part the result of microbial evolutionary developments and of the progressive biotic colonization of the land.
 
Article
The inability to control successfully the world's rapidly increasing human population has led to further study of intrauterine devices. This article discusses the current knowledge of intrauterine contraception and its prospects for the future. It considers intrauterine contraception as an evolving method, and emphasizes the problems that accompany IUD use and the kinds of modifications that may improve their performance.
 
Article
Direct energy coupling in mitochondria requires the participation of intrinsic ionophores. These protein-linked ionophores are now demonstrable and isolatable. The central phenomena of energy coupling, such as how uncouplers act, how coupling in cytochrome oxidase is mediated, and how ATP is synthesized, can be satisfactorily rationalized in terms of these intrinsic ionophores.
 
Article
For the past decade, the scientific and popular press have carried frequent articles about a catastrophic mass extinction that supposedly destroyed the majority of the earth's species, including the dinosaurs, approximately 65 million years ago. Since 1980, more than 2000 papers and books have dealt with some aspect of a mass extinction at the Cretaceous-Tertiary (K/T) boundary. One authoritative estimate of the severity of the extinctions is that 60-80% of all the living species became extinct at this boundary (Raup 1988). There appears to be a general acceptance of the fact that such a great catastrophe did occur. Most of the argument among scientists now is devoted to the determination of the cause. In this article, I argue that the species changes at the K/T boundary were neither sudden nor catastrophic. They were most likely caused by a regression of sea level that led to a decrease in primary production. NASA Edited
 
Article
Plant scientists have sought to maximize the yield of food crops since the beginning of agriculture. There are numerous reports of record food and biomass yields (per unit area) in all major crop plants, but many of the record yield reports are in error because they exceed the maximal theoretical rates of the component processes. In this article, we review the component processes that govern yield limits and describe how each process can be individually measured. This procedure has helped us validate theoretical estimates and determine what factors limit yields in optimal environments.
 
Top-cited authors
Frederick J. Swanson
  • Oregon State University
John Aber
  • University of New Hampshire
Kenneth Cummins
  • Humboldt State University
J. David Allan
  • University of Michigan
Richard E. Sparks
  • University of Illinois, Urbana-Champaign