Why should cell biologists study microbial pathogens?

One quarter of all deaths worldwide each year result from infectious diseases caused by microbial pathogens. Pathogens infect and cause disease by producing virulence factors that target host cell molecules. Studying how virulence factors target host cells has revealed fundamental principles of cell biology. These include important advances in our understanding of the cytoskeleton, organelles and membrane-trafficking intermediates, signal transduction pathways, cell cycle regulators, the organelle/protein recycling machinery, and cell-death pathways. Such studies have also revealed cellular pathways crucial for the immune response. Discoveries from basic research on the cell biology of pathogenesis are actively being translated into the development of host-targeted therapies to treat infectious diseases. Thus there are many reasons for cell biologists to incorporate the study of microbial pathogens into their research programs.     

Human fungal pathogens: Why should we learn?

Human fungal pathogens that cause invasive infections are hidden killers, taking lives of one and a half million people every year. However, research progress in this field has not been rapid enough to effectively prevent or treat life-threatening fungal diseases. To update recent research progress and promote more active research in the field of human fungal pathogens, eleven review articles concerning the virulence mechanisms and host interactions of four major human fungal pathogens–Candida albicans, Cryptococcus neoformans, Aspergillus fumigatus, and Histoplasma capsulatum–are presented in this special issue.     

Botanical literacy: What and how should students learn about plants?

Botanists benefit from a scientifically literate society and an interested and botanically literate student population, and we have opportunities to promote literacy in our classes. Unfortunately, scientific illiteracy exists, in part, because students are technologically advanced but lack intellectual curiosity and rigor. Botanical illiteracy results from several interacting factors, including a lack of interest in plants and infrequent exposure to plant science before students reach college. If scientific or botanical literacy is a goal, we must understand what literacy means and how we can help students reach that goal. A model of biological literacy recognizes four levels; students enter courses at the lowest level possessing misconceptions about concepts; however, misconceptions can be used to our advantage, especially by using concept inventories. Inquiry-based instruction is advocated for all science courses, and learning theory supports inquiry. Seven principles of learning inform recommendations about how botanists should teach, including using themes and "thinking botanically" to illustrate all biological concepts. Overall, consideration of the botanical content taught is less critical than the methods used to teach that content. If botanists emphasize thinking and process skills with an understanding of concepts, we will prepare scientifically literate students and citizens and benefit from our efforts.     

Fisheries in Chinese seas: What can we learn from controversial official fisheries statistics?

China (excluding Hong Kong, Macao and Taiwan, unless specified) is the greatest contributor to the total catch of global marine fisheries. As such, data about the degrees of exploitation and developmental dynamics of its fisheries are essential to evaluate and guide future sustainable seafood production and policy implementation and adjustments. In this study, we summarized the national official statistic data on domestic marine fisheries (including both marine capture fisheries and mariculture) from the earliest available year, 1950, to the latest year, 2014, using on the China Fishery Statistical Yearbooks. We also conducted analyses to understand the historical and current statuses of Chinese marine fisheries and their developmental trends. Domestic marine capture fisheries are declining and will continue to decline because of the current degradation and loss of coastal habitats, mainly due to coastal development and pollution and the over-exploitation of coastal natural resources. In contrast, mariculture has demonstrated promise as an approach to increase seafood production. However, given the wide latitudinal range of domestic seas in China, global climate change may impact China’s marine natural resources. We highlight that effective management measures and long-term monitoring are essential for the sustainability of domestic marine capture fisheries. Moreover, environmentally-friendly practices in mariculture should be enhanced and species introduction carefully monitored to achieve sustainable development.     

Ventilation inhomogeneity during controlled ventilation. Which index should be used?

Six indexes for diagnosing uneven ventilation by tracer gas washout were studied. The indexes were lung clearance index, mixing ratio, Becklake index, multiple-breath alveolar mixing inefficiency, moment ratio, and pulmonary clearance delay, all of which increase with impaired pulmonary gas mixing. In model lung tests, indexes that compared the actual washout curve with a calculated ideal curve (mixing ratio, multiple-breath alveolar mixing inefficiency, and pulmonary clearance delay) were unaffected by changes in tidal volume and series dead space, whereas the others varied markedly. In both spontaneously breathing and mechanically ventilated patients all indexes showed a significant difference between smokers and nonsmokers (P less than 0.002), but the indexes were somewhat different in their assessment of different ventilatory patterns. However, the mean value for all indexes, with the exception of mixing ratio, was smallest with a fast insufflation followed by an end-inspiratory pause. Any of the indexes may be useful if its limitations are recognized, but mixing ratio, multiple-breath alveolar mixing inefficiency, and pulmonary clearance delay seem preferable, because they are not affected by changes in tidal volume and dead space fraction.     

Which fields under a coverslip should one assess to estimate sperm motility?

Under field conditions the motility of bull semen often has to be estimated under a coverslip on a microscope slide. This study was aimed at determining which combination of fields under coverslips provides measurements of sperm motility that best represent the motility in semen specimens as measured in a specially designed chamber for use in a computer-assisted sperm analyzer (CASA). We measured the motility (percentages motile, progressively motile, and aberrantly motile spermatozoa) in each of four straws of frozen-thawed semen from each of 10 bulls five times, ranging from 5 to 120 minutes after thawing with each bull by straw by time combination yielding one semen specimen. Motility was measured in duplicate in a Hamilton, Thorne IVOS CASA; once in each of 12 fields equally spaced along the equatorial radius of a coverslip (Field 0 at the edge and Field 11 at the center) and once in each of eight equally spaced fields along the equator of a Leja 4 chamber designed for use in a CASA. We used the weighted average motility of all fields in a chamber as gold standard and compared it to the average motility of each the following combinations of fields under the coverslip: all 12 fields, Fields 2 to 4, Fields 2 and four, Field 3 and the center three fields. The concordance correlation coefficient (CCC) was determined between the motility in each combination of fields under coverslips and the chambers as a reproducibility index, which evaluates the agreement between the readings under the coverslips and the gold standard readings in the chambers (n = 187 for each CCC). We performed pairwise comparisons of the CCCs (P < 0.005 for each comparison) and established that the average motility under all 12 fields better reproduced the motility in the chamber than the center three fields or Field 3. The averages of Fields 2 to 4 and Fields 2 and 4 reproduced chamber motility as well as the average of all 12 fields, except for the percentage motile sperm, where the average of all 12 fields was better. Using the average motility of Fields 2 and 4, 50% of estimates fell within 6%, 4% and 3% above or below the percentages motile, progressively motile and aberrantly motile spermatozoa in the Leja 4 chamber, 80% of estimates fell within 12%, 8% and 7% thereof and 95% fell within 23%, 13% and 12% thereof. In conclusion, for the method of spreading semen under a coverslip and the range in motility values used, this study shows that the average of the motility over the 12 fields along the equatorial radius under a coverslip provides the best estimate of the motility of a semen specimen, while the average of Fields 2 and 4 is also suitable for the subjective estimation of motility under field conditions, although the estimated motility is expected to fall within 6% above or below the motility of the specimen in only 50% of semen specimens.     

Why should many skeletal scientists and clinicians learn the Utah paradigm of skeletal physiology?

Adding later facts and ideas to a universally accepted "1960 paradigm" of skeletal physiology led to the still-evolving "Utah paradigm". The ASBMR's William Neuman award in 2001 to one of the latter paradigm's architects (HMF) suggested that physiologists began to view it as a valid supplement to its predecessor. Nevertheless it diffused poorly among most SSCs (Skeletal Scientists and Clinicians, plus all others who work in any way on skeletal matters), even though success in the quest for knowledge and recognition by many of them could depend on learning that paradigm's insights. Those insights can help to minimize serious errors in some experimental designs and in interpreting some kinds of data. To explain how success in that quest could depend on the Utah paradigm requires explaining the nature of the above errors, some features of both paradigms, some implications of the newer one, and when that quest's success might not require knowing the Utah paradigm. A three-part message distilled from the past for present and future SSCs concludes the article. It took decades to understand such things and find effective ways to explain them, and both matters probably need improvement (to paraphrase Pogo, "We met the enemy and perhaps it was us more than them"). During those decades the author changed from an active SSC hunter-player to a spectator, known to some as a feisty eccentric old dinosaur (FEOD) (Note A). So here a voice from the past would speak to present and future SSCs.     

Strong spatial genetic structure in five tropical Piper species: should the Baker–Fedorov hypothesis be revived for tropical shrubs?

Fifty years ago, Baker and Fedorov proposed that the high species diversity of tropical forests could arise from the combined effects of inbreeding and genetic drift leading to population differentiation and eventually to sympatric speciation. Decades of research, however have failed to support the Baker-Fedorov hypothesis (BFH), and it has now been discarded in favor of a paradigm where most trees are self-incompatible or strongly outcrossing, and where long-distance pollen dispersal prevents population drift. Here, we propose that several hyper-diverse genera of tropical herbs and shrubs, including Piper (>1,000 species), may provide an exception. Species in this genus often have aggregated, high-density populations with self-compatible breeding systems; characteristics which the BFH would predict lead to high local genetic differentiation. We test this prediction for five Piper species on Barro Colorado Island, Panama, using Amplified Fragment Length Polymorphism (AFLP) markers. All species showed strong genetic structure at both fine- and large-spatial scales. Over short distances (200-750 m) populations showed significant genetic differentiation (Fst 0.11-0.46, P < 0.05), with values of spatial genetic structure that exceed those reported for other tropical tree species (Sp = 0.03-0.136). This genetic structure probably results from the combined effects of limited seed and pollen dispersal, clonal spread, and selfing. These processes are likely to have facilitated the diversification of populations in response to local natural selection or genetic drift and may explain the remarkable diversity of this rich genus.     

Microbial genomics: tropical treasure?

A Brazilian consortium has unveiled the genomic DNA sequence of the purple-pigmented bacterium Chromobacterium violaceum, a dominant component of the tropical soil microbiota. The sequence provides insight into the abundant potential of this organism for biotechnological and pharmaceutical applications.     

Are tropical butterflies more colorful?

There is a common and long-standing belief that tropical butterflies are more striking in their coloration than those of cooler climates. It has been suggested that this is due to more intense biotic selection or mate selection in the tropics. We tested whether there were differences in coloration by examining the dorsal surface color properties of male butterflies from three regions of the western hemisphere: the Jatun-Satcha Reserve in lowland Ecuador (tropical), the state of Florida, USA (subtropical) and the state of Maine, USA (cool temperate). We digitally photographed the dorsal wing and body surface of male butterfly specimens from Maine, Florida, and Ecuador. For each photograph, we analyzed the mean and variation for the color-parameters that are thought to be related to colorfulness; namely Hue, saturation and intensity. Overall, the Ecuadorian sample exhibited more varied intensity, saturation, and Hue compared to the other regions. These results suggest a more complex assemblage of colors and patterns regionally and on a butterfly-by-butterfly basis in the tropics. The greater complexity of colors within each butterfly in our Ecuadorian sample suggests that tropical butterflies are indeed more ‘colorful’, at least by some measures. Possible reasons for this include stronger predation pressure selecting for aposematism, greater species diversity selecting for camouflage or warning coloration against potential predators, and easier recognition of potential mates in a species rich environment.     

Coevolution between flight morphology,vertical stratification and sexual dimorphism: what can we learn from tropical butterflies?

Occurrence patterns are partly shaped by the affinity of species with habitat conditions. For winged organisms, flight‐related attributes are vital for ecological performance. However, due to the different reproductive roles of each sex, we expect divergence in flight energy budget, and consequently different selection responses between sexes. We used tropical frugivorous butterflies as models to investigate coevolution between flight morphology, sex dimorphism and vertical stratification. We studied 94 species of Amazonian fruit‐feeding butterflies sampled in seven sites across 3341 ha. We used wing–thorax ratio as a proxy for flight capacity and hierarchical Bayesian modelling to estimate stratum preference. We detected a strong phylogenetic signal in wing–thorax ratio in both sexes. Stouter fast‐flying species preferred the canopy, whereas more slender slow‐flying species preferred the understorey. However, this relationship was stronger in females than in males, suggesting that female phenotype associates more intimately with habitat conditions. Within species, males were stouter than females and sexual dimorphism was sharper in understorey species. Because trait–habitat relationships were independent from phylogeny, the matching between flight morphology and stratum preference is more likely to reflect adaptive radiation than shared ancestry. This study sheds light on the impact of flight and sexual dimorphism on the evolution and ecological adaptation of flying organisms.     

Are tropical fungal endophytes hyperdiverse?

Fungal endophytes are ubiquitous fungi that inhabit healthy plant tissues without causing disease. Endophytes have been found in every plant species examined to date and may be important, but often overlooked, components of fungal biodiversity. In two sites in a lowland, moist tropical forest of central Panama, we quantified endophyte colonization patterns, richness, host preference, and spatial variation in healthy leaves of two co-occurring, understory tree species [ Heisteria concinna (Olacaceae) and Ouratea lucens (Ochnaceae)]. From 83 leaves, all of which were colonized by endophytes, we isolated 418 endophyte morphospecies (estimated 347 genetically distinct taxa), most of which were represented by only a single isolate (59%). Among morphospecies encountered in more than one leaf (nonsingletons), we found evidence of host preference and spatial heterogeneity using both morphospecies frequencies and presence/absence records. Based on these data, we postulate that tropical endophytes themselves may be hyperdiverse and suggest that extrapolative estimates that exclude them will markedly underestimate fungal species diversity.