Teaching "Species"

A clear understanding of the term "species" is fundamental to the subject of evolution. However, introductory textbooks often fail to address this topic until one of the later chapters, after having used the term species in all preceding chapters. Furthermore, definitions of terms critical to a clear understanding of this subject are often vague or absent in chapters on species concepts. We feel the popular notion of a "species problem" has been unnecessarily inflated by this less-than-effective educational approach. Clearly addressing this essential subject at the beginning of a course on evolution will prepare students to learn the details and complexities of evolution. Here we provide the background for an alternative approach to this foundational topic, followed by an outlined lesson plan. We emphasize early introduction of this subject in texts and courses using unambiguous terminology and including the historical development of species concepts.     

"I" becomes "L": modification of vertical mammaplasty

The problems of the vertical mammaplasty by Lejour (i.e., gathering the skin envelope in one vertical suture, frequent secondary healing problems, and later sagging of the inferior glandular part in the case of large and very large breasts) are well known. A simple modification of the Lejour technique, that is, adding a lateral inframammary scar to shorten the vertical scar length, is presented. The modified L technique was used in 45 patients (90 breasts) between October of 1999 and August of 2001. With an average follow-up of 13 months, the jugular notch-to-nipple distance was 21 cm, the vertical scar length was 8.4 cm, the lateral inframammary scar length was 11 cm, and the average resection weight was 625 g per breast (range, 200 g to 2080 g). Even among patients who had very large glandular bases and resection weights it was possible to achieve a breast base reduction, modeling the glandular corpus to a harmonic, well-projecting, and youthful shape. Slight wound-healing problems with spontaneous cicatrization within 2 weeks occurred in six patients. In two patients who exhibited gigantomastia up to 2080 g per breast, partial mamilla necrosis occurred on one side. Ninety-one percent of the patients reported being "very satisfied" with the outcome, and 9 percent reporting being "satisfied." The authors' modification of the vertical mammaplasty to an L-shaped scar technique enables the surgeon to apply the principles of the Lejour technique for higher resection weights and diminishes wound-healing problems, and it is still a scar-minimizing technique that results in a scar-free cleavage. It is easy to learn and an ideal standard technique for a teaching hospital.     

cAMP regulation of "pathogenic" and "saprophytic" fungal spore germination

We report on the elucidation of two separate pathways of spore germination in a plant pathogenic fungus Colletotrichum gloeosporioides f. sp. aeschynomene. Conidia of the fungus can germinate either from one side or from both sides, depending on external conditions. In shake culture that includes an extract made up from fresh peas, the unicellular conidium divides and one of the two cells develops a germ tube. On a solid surface this germ tube differentiates an appressorium. In rich medium without pea extract, germination is highly similar to Aspergillus spore germination: the conidium swells, forms a single germ tube and then divides and forms a second germ tube. Conidia that germinate in a rich medium do not form appressoria even on a solid surface and are non-pathogenic. In rich medium, cAMP stimulates germination in rich liquid cultures and induces appressoria formation on a hard surface. In pea extract cAMP induces swelling and formation of irregular germ tubes and appressoria. Our results suggest that plant surface signals induce pathogenic-specific spore germination in a cAMP-independent manner. cAMP is required for saprophytic germination and for appressorium formation.     

Cognizing "Cognized Models"

In his later work Rappaport acknowledged that his earlier efforts had overemphasized organic and ecological functions in the explanation of cultural phenomena. He then distanced himself from both idealism and reductive materialism and set out to understand the complexities of cultural understandings and ritual. Specifically, he shifted from functionalism to formalism in an effort to understand ritual and its language in relation to cultural norms. Ultimately his analysis was implicitly structural, understanding the part as a constituent of an overarching arrangement and in terms of what Althusser would have called "structural causality." Although his work benefited from this shift from function to structure, Rappaport did not use it to explore the political dimension. However, a holistic ecology such as the one Rappaport essayed must ultimately embrace both political ecology and historical ecology, [cognized models, ritual, political ecology, structural causality-]     

"DRUMMING" BY SWIFTS

On 27 April 1958, while my wife and I were watching a party of 20–30 Mottled Swifts Apus aequatorialis over a dam ten miles west of Nairobi, Kenya, we repeatedly heard quite a loud "prrrpt-prrrpt-prrrpt". We discovered that the swifts were making this noise by spreading and slightly depressing their tails and moving them sideways so that the outer feather was almost parallel with the wing. The 'leading' feather thus projected into the slipstream was quite clearly seen to vibrate at the same time as the noise was heard. We watched this performance for about half an hour and noted that the tails were invariably turned to the right; we were both using binoculars. We saw that several birds were performing in this manner but it did not appear to be in connection with any display towards any other particular member of the party. The sexes of the Mottled Swift are indistinguishable in the field. The 'drumming' took place in the early part of the dive towards the surface of the dam from which the birds were drinking on the wing; it did not appear to cause any deflection of the flight path.     

"Zigzag" wavy-line periareolar incision

There is almost no mention of improvement in the aesthetics of areolar incisions in the plastic and reconstructive surgery literature. The most visible area of the breast is the central mound; therefore, it behooves surgeons to make an areolar incision as inconspicuous as possible. Minimal incision breast operations and short-scar operations, such as mastopexy and vertical reduction mammaplasty, use a circumareolar incision. This circumareolar technique, which specifically avoids a purse-string support suture, is useful in all periareolar incisions. This method creates a scar that mimics the elusive, natural irregularity between the areola and periareolar skin. The goal is to have an irregular, random, wavy line that appears more natural. Between August of 1998 and August of 1999, 104 "zigzag" wavy-line procedures were performed. The complications seen in this series included delayed healing in four patients and hypertrophic scar in two patients. No scars were surgically revised. The results demonstrated a definite difference compared to a circular scar. The zigzag wavy-line technique complements the innovative methods that shorten scars while they create a more natural, lasting breast mound. For areolar incisions, good results are deceptively subtle, but unnatural results can be painfully obvious. The zigzag wavy-line incision subtly eludes the eye in diminishing the signs the patient has undergone an operation.     

Comparative genomics of "Dehalococcoides ethenogenes" 195 and an enrichment culture containing unsequenced "Dehalococcoides" strains

Tetrachloroethene (PCE) and trichloroethene (TCE) are prevalent groundwater contaminants that can be completely reductively dehalogenated by some "Dehalococcoides" organisms. A Dehalococcoides-organism-containing microbial consortium (referred to as ANAS) with the ability to degrade TCE to ethene, an innocuous end product, was previously enriched from contaminated soil. A whole-genome photolithographic microarray was developed based on the genome of "Dehalococcoides ethenogenes" 195. This microarray contains probes designed to hybridize to >99% of the predicted protein-coding sequences in the strain 195 genome. DNA from ANAS was hybridized to the microarray to characterize the genomic content of the ANAS enrichment. The microarray results revealed that the genes associated with central metabolism, including an apparently incomplete carbon fixation pathway, cobalamin-salvaging system, nitrogen fixation pathway, and five hydrogenase complexes, are present in both strain 195 and ANAS. Although the gene encoding the TCE reductase, tceA, was detected, 13 of the 19 reductive dehalogenase genes present in strain 195 were not detected in ANAS. Additionally, 88% of the genes in predicted integrated genetic elements in strain 195 were not detected in ANAS, consistent with these elements being genetically mobile. Sections of the tryptophan operon and an operon encoding an ABC transporter in strain 195 were also not detected in ANAS. These insights into the diversity of Dehalococcoides genomes will improve our understanding of the physiology and evolution of these bacteria, which is essential in developing effective strategies for the bioremediation of PCE and TCE in the environment.     

"Competence" progress

Zwang et al. (2011) have identified outputs of two EGF pulses that commit cells to cycle. The first induces components for lipid biosynthesis and sets up an inhibitory latch through p53. The second works through ERK to EGR1 and releases the latch to promote restriction point traverse.     

Supramolecular photochemical self-assemblies for fluorescence "turn on" and "turn off" assays for chem-bio-helices.

We describe the development of an optical sensing system for the high-throughput screening (HTS) of a broad range of biological molecules, whole cells, organisms and pathogens, and illustrate the technology applications by a hyaluronidase enzyme activity assay as a specific example. At the core of the technology described in this paper, is the exciton concept that is relevant to molecular aggregation. J-aggregates of cyanine dyes have a narrower, red-shifted absorption band compared to monomer. We demonstrate that self-assembly may be driven by the helicogenic nature of the cyanine dye, converting the linear polymers of hyaluronic acid or carboxymethyl cellulose into supramolecular helical assemblies. This self-assembly is accompanied by an intense, sharp, red-shifted J-aggregate fluorescence. We utilized this property to develop an assay for the enzyme hyaluronidase, based upon the concept of "scaffold destruction," whereby the disruption/destruction of the hyaluronic acid polymer by hyaluronidase is accompanied by an attenuation of light emission from the J-aggregate. The extent of light attenuation provides an index of hyaluronidase activity. Other polymers of carbohydrates, proteins, nucleic acids and chemical polymers (such as the carbon nanotube) might provide a similar scaffold for helicogenic dyes upon which molecular aggregation can occur. A key feature of these assays is that they are label-free.     

Maladaptive "gambling" by pigeons

When humans buy a lottery ticket or gamble at a casino they are engaging in an activity that on average leads to a loss of money. Although animals are purported to engage in optimal foraging behavior, similar sub-optimal behavior can be found in pigeons. They show a preference for an alternative that is associated with a low probability of reinforcement (e.g., one that is followed by a red hue on 20% of the trials and then reinforcement or by a green hue on 80% of the trials and then the absence of reinforcement) over an alternative that is associated with a higher probability of reinforcement (e.g., blue or yellow each of which is followed by reinforcement 50% of the time). This effect appears to result from the strong conditioned reinforcement associated with the stimulus that is always followed by reinforcement. Surprisingly, although it is experienced four times as much, the stimulus that is never followed by reinforcement does not appear to result in significant conditioned inhibition (perhaps due to the absence of observing behavior). Similarly, human gamblers tend to overvalue wins and undervalue losses. Thus, this animal model may provide a useful analog to human gambling behavior, one that is free from the influence of human culture, language, social reinforcement, and other experiential biases that may influence human gambling behavior.     

Short electric-field pulses convert DNA from "condensed" to "free" conformation

Electric-field pulses of e.g. 20 kV/cm and 100 μs induce a strong decrease in the scattered light intensity of DNA condensed by spermine. Analysis of this effect demonstrates that the decrease of the scattered light intensity results from decondensation of DNA. The decondensation reaction requires an electric-field strength exceeding a threshold value. Complete decondensation can be achieved at field strength that are only slightly higher than the threshold value. The decondensation process is strongly accelerated at high electric-field strengths. At 30 kV/cm, the decondensation time constant is ～8 μs, corresponding to an acceleation factor of 10⁵ relative to the field-free decondensation reaction. The dependence of the time constants on the electric-field strength suggests that the field-induced decondensation is due to a dissociation field effect. The condensation process observed after electric-field pulses at low concentrations of DNA and spermine shows a characteristic induction period, which strongly depends on the spermine concentration. This induction period reflects the time required for the binding of spermine to DNA, until the degree of binding is sufficiently high for the condensation reaction. The fast dissociation of condensed DNA by electric-field pulses together with a relatively long lifetime of the free DNA results in a reaction cycle resembling a hysteresis loop.     

Current "corrected" calcium concept challenged.

There is wide individual variation in the number of millimoles of calcium bound per gram of albumin in the serum. Individual regression coefficients for serum calcium concentration on serum albumin concentration have been determined in 62 people (25 of our own patients and 37 reported by others). The 95 percentile range was 0-007-0-053 mmol/g, with a median value of 0-025 mmol/g. Accordingly, it is not valid to "correct" a person''s measured serum total calcium concentration for variations in serum albumin concentration using an average regression coefficient. Rather, the individual''s own regression coefficient must be used. A tourniquet test seems to be the simplest technique for determining this value. Even then, precise interpretation of an individual''s corrected serum calcium concentration is possible only when an appropriate reference range for corrected serum calcium concentration has been established. Such an appropriate reference range must be determined from an adequate number of normal people using the individual''s own correction factor in each case.     

"Halo nevi" and UV radiation

Halo nevi, also termed Sutton nevi, are defined as benign melanocytic nevi that are surrounded by an area of depigmentation resembling a halo. Halo nevi are common in children and young adults, with a mean age at onset of 15 years. The incidence in the population is estimated to be approximately 1%. Affected individuals frequently have multiple lesions which are usually localized on the back. A familial tendency for halo nevi has been reported. The etiology of halo nevi is unknown. It is an autoimmune response and T lymphocytes are considered to play a key role in the progressive destruction of nevus cells. Halo nevi may be associated with autoimmune disorders such as vitiligo, Hashimoto thyroiditis, alopecia areata, celiac disease, atopic dermatitis and others. It has been proved that halo nevi are detected after an intense sun exposure especially after sunburns. The etiology of halo nevi, association with malignant melanoma and the role of sun exposure in the development of halo nevi are discussed.     

Coding "what" and "when" in the Archer fish retina

Traditionally, the information content of the neural response is quantified using statistics of the responses relative to stimulus onset time with the assumption that the brain uses onset time to infer stimulus identity. However, stimulus onset time must also be estimated by the brain, making the utility of such an approach questionable. How can stimulus onset be estimated from the neural responses with sufficient accuracy to ensure reliable stimulus identification? We address this question using the framework of colour coding by the archer fish retinal ganglion cell. We found that stimulus identity, “what”, can be estimated from the responses of best single cells with an accuracy comparable to that of the animal''s psychophysical estimation. However, to extract this information, an accurate estimation of stimulus onset is essential. We show that stimulus onset time, “when”, can be estimated using a linear-nonlinear readout mechanism that requires the response of a population of 100 cells. Thus, stimulus onset time can be estimated using a relatively simple readout. However, large nerve cell populations are required to achieve sufficient accuracy.

Authors Summary

In our interaction with the environment we are flooded with a stream of numerous objects and events. Our brain needs to understand the nature of these complex and rich stimuli in order to react. Research has shown ways in which a ‘what’ stimulus was presented can be encoded by the neural responses. However, to understand ‘what was the nature of the stimulus’ the brain needs to know ‘when’ the stimulus was presented. Here, we investigated how the onset of visual stimulus can be signalled by the retina to higher brain regions. We used archer fish as a framework to test the notion that the answer to the question of ‘when’ something has been presented lies within the larger cell population, whereas the answer to the question of ‘what’ has been presented may be found at the single-neuron level. The utility of the archer fish as model animal stems from its remarkable ability to shoot down insects settling on the foliage above the water level, and its ability to distinguish between artificial targets. Thus, the archer fish can provide the fish equivalent of a monkey or a human that can report psychophysical decisions.     

The use of multifolded pericranial flaps as "plugs" and "pads"

Pericranial flaps are thin and, hence, their volumes are small. Therefore, their use for soft-tissue augmentation has not been popular. In this article, the author introduces a new concept: the use of a multifolded pericranial flap as a "plug" or a "pad" for localized contour defects. Eight patients were included in the study. In all cases, an anteriorly based pericranial flap was used, and the flap was folded on itself several times to increase its bulk. The results were satisfactory in all patients. The literature on the topic is reviewed, and the blood supply of pericranial flaps is discussed.     

X-ray crystallographic observation of "in-line" and "adjacent" conformations in a bulged self-cleaving RNA/DNA hybrid

The RNA strand in an RNA/DNA duplex with unpaired ribonucleotides can undergo self-cleavage at bulge sites in the presence of a variety of divalent metal ions (Hüsken et al., Biochemistry, 1996, 35:16591-16600). Transesterification proceeds via an in-line mechanism, with the 2'-OH of the bulged nucleotide attacking the 3'-adjacent phosphate group. The site-specificity of the reaction is most likely a consequence of the greater local conformational freedom of the RNA backbone in the bulge region. A standard A-form backbone geometry prohibits formation of an in-line arrangement between 2'-oxygen and phosphate. However, the backbone in the region of an unpaired nucleotide appears to be conducive to an in-line approach. Therefore, the bulge-mediated phosphoryl transfer reaction represents one of the simplest RNA self-cleavage systems. Here we focus on the conformational features of the RNA that underlie site-specific cleavage. The structures of an RNA/DNA duplex with single ribo-adenosyl bulges were analyzed in two crystal forms, permitting observation of 10 individual conformations of the RNA bulge moiety. The bulge geometries cover a range of relative arrangements between the 2'-oxygen of the bulged nucleotide and the P-O5' bond (including adjacent and near in-line) and give a detailed picture of the conformational changes necessary to line up the 2'-OH nucleophile and scissile bond. Although metal ions are of crucial importance in the catalysis of analogous cleavage reactions by ribozymes, it is clear that local strain or conformational flexibility in the RNA also affect cleavage selectivity and rate (Soukup & Breaker, RNA, 1999, 5:1308-1325). The geometries of the RNA bulges frozen out in the crystals provide snapshots along the reaction pathway prior to the transition state of the phosphoryl transfer reaction.     

Linkage analysis of "necessary" disease loci versus "susceptibility" loci.

The association of some diseases with specific alleles of certain genetic markers has been difficult to explain. Several explanations have been proposed for the phenomenon of association, e.g. the existence of multiple, interacting genes (epistasis) or a disease locus in linkage disequilibrium with the marker locus. One might suppose that when marker data from families with associated diseases are analyzed for linkage, the existence of the association would assure that linkage will be found, and found at a tight recombination fraction. In fact, however, linkage analyses of some diseases associated with HLA, as well as diseases associated with alleles at other loci located throughout the genome, show significant evidence against linkage, and others show loose linkage, to the puzzlement of many researchers. In part, the puzzlement arises because linkage analysis is ideal for looking for loci that are necessary, even if not sufficient, for disease expression but may be much less useful for finding loci that are neither necessary nor sufficient for disease expression (so-called susceptibility loci). This work explores what happens when one looks for linkage to susceptibility loci. A susceptibility locus in this case means that the allele increases risk but is neither necessary nor sufficient for disease expression. It might be either an allele at the marker locus itself that is increasing susceptibility or an allele at a locus in linkage disequilibrium with the marker. This work uses computer simulation to examine how linkage analyses behave when confronted with data from such a model.(ABSTRACT TRUNCATED AT 250 WORDS)     

"Craziness" and "visions": experiences after a stroke.

For a stroke victim there may be at least three types of strange occurrences: incorrect saying, seeing, and thinking. To the patient only the third seems to be "crazy". After a stroke (left hemisphere), which mainly produced serious aphasia, I (the patient) felt crazy two or three times when someone said something I expected him to say. On the other hand, my initial aphasic "gibberish speech" and an occasional false vision did not seem crazy. In my case the vision is always a car or a child, seen on my extreme right, where I am otherwise blind from the stroke. I am always driving when it happens; in recent years this phenomenon occurs when I am tired or tense, or the light is poor. These rapid visions do not seem insane but merely physical problems in my eyes, much like ordinary people''s dreams.     

Alpha-glucosidase mutant catalyzes "alpha-glycosynthase"-type reaction

Replacement of the catalytic nucleophile Asp481 by glycine in Schizosaccharomyces pombe alpha-glucosidase eliminated the hydrolytic activity. The mutant enzyme (D481G) was found to catalyze the formation of an alpha-glucosidic linkage from beta-glucosyl fluoride and 4-nitrophenyl (PNP) alpha-glucoside to produce two kinds of PNP alpha-diglucosides, alpha-isomaltoside and alpha-maltoside. The two products were not hydrolyzed by D481G, giving 41 and 29% yields of PNP alpha-isomaltoside and alpha-maltoside, respectively. PNP monoglycosides, such as alpha-xyloside, alpha-mannoside, or beta-glucoside, acted as the substrate, but PNP alpha-galactoside and maltose could not. No detectable product was observed in the combination of alpha-glucosyl fluoride and PNP alpha-glucoside. This study is the first report on an "alpha-glycosynthase"-type reaction to form an alpha-glycosidic linkage.