Taxonomy and biogeography of the fiddler crabs (Ocypodidae: Genus Uca) of the Atlantic and Gulf coasts of eastern North America

Fifteen species of fiddler crabs are reported for eastern North America between Massachusetts and Quintana Roo, Mexico. Thirteen occur in the United States and 11 in Mexico, with eight in common to the two countries. Of 13 species in the Gulf of Mexico, five are endemic and a sixth is restricted largely to the peninsulas of Florida and Yucatan. The status of U. rapax in the northern Gulf remains to be resolved. Range limits of most species approximate one or the other of two sets of intersecting thermal and geological boundaries that subdivide the Gulf of Mexico along north-south and east-west axes. Species belonging to subgenus Minuca tend to replace one another at the thermally-controlled Carolinian-Caribbean marine biotic boundary across the Florida peninsula and northern Gulf. However, only U. minax of all the North American fiddler crabs exhibits the classical disjunct Carolinian distribution, and this appears basically to reflect the discontinuous distribution of temperate salt marshes that are the habitat of the species. Distributions of species belonging to subgenus Celuca adhere for the most part to the subdivision of the Gulf into western terrigenous and eastern carbonate sedimentary provinces. The northern transition occurs in the vicinity of Apalachee Bay and the southern at Laguna de Terminos. A third distributional pattern is shown by U. subcylindrica , a specialized endemic species of the hypersaline Laguna Madre system of the western Gulf. The level of endemism in the fiddler crabs is relatively high in comparison with that of other marine groups within the Gulf of Mexico. This may be a consequence of the adaptations of fiddler crabs as specialized deposit feeders to regional differences in climatic and edaphic characteristics of a marginally marine upper shore habitat. The distributional patterns of the endemics could prove useful in reconstructing palaeoecological events of evolutionary significance within the Gulf of Mexico.     

Carboxylic acids in crystallization of macromolecules: learning from successful crystallization experiments

The production of macromolecular crystals suitable for structural analysis is one of the most important and limiting steps in the structure determination process. Often, preliminary crystallization trials are performed using hundreds of empirically selected conditions. Carboxylic acids and/or their salts are one of the most popular components of these empirically derived crystallization conditions. Our findings indicate that almost 40 % of entries deposited to the Protein Data Bank (PDB) reporting crystallization conditions contain at least one carboxylic acid. In order to analyze the role of carboxylic acids in macromolecular crystallization, a large-scale analysis of the successful crystallization experiments reported to the PDB was performed. The PDB is currently the largest source of crystallization data, however it is not easily searchable. These complications are due to a combination of a free text format, which is used to capture information on the crystallization experiments, and the inconsistent naming of chemicals used in crystallization experiments. Despite these difficulties, our approach allows for the extraction of over 47,000 crystallization conditions from the PDB. Initially, the selected conditions were investigated to determine which carboxylic acids or their salts are most often present in crystallization solutions. From this group, selected sets of crystallization conditions were analyzed in detail, assessing parameters such as concentration, pH, and precipitant used. Our findings will lead to the design of new crystallization screens focused around carboxylic acids.     

Using wavelet analysis to examine bark microrelief

Key Message

An improved quantification of variations in bark microrelief is presented that uses wavelets on a circular domain from data acquired using the LaserBark? automated tree measurement system.

Abstract

An important metric of canopy structure, bark microrelief affects both the hydrology and biogeochemistry of forests. Increased bark microrelief leads to reduced stemflow volumes and higher concentrations of stemflow leachates and nutrient-ions. Consequently, an improved representation of bark microrelief would be useful to describe the influence of various tree species on water and solute contributions to the forest floor. Most existing methods to quantify bark microrelief are ‘global’ measures; that is, they provide a single number that represents the overall bark microrelief of the entire perimeter of the tree. To remedy this, wavelet analysis of LaserBark? automated tree measurement system data is proposed and described to quantify variations in bark microrelief around the perimeter of the tree. This measure describes the spatial differences in bark microrelief and allows representation of trees that exhibit directional variability in bark microrelief due to natural or anthropogenic effects. The results show that wavelet analysis is effective in quantifying both bark microrelief and large-scale tree asymmetry. The radial component highlights changes in the depth of bark microrelief while the tangential component relates to the distance between bark furrows in the bark cross section. Thus, wavelet analysis may be a useful tool for comparing bark structure that varies, for example, within- and between-tree species, at different stages of tree growth, and among trees grown under different environmental conditions.     

Characterization of a glucuronyltransferase: neolactotetraosylceramide glucuronyltransferase from rat brain

The properties of a rat brain glucuronyltransferase, which is presumed to be associated with the biosynthesis of the HNK-1 epitope on sulfoglucuronyl glycolipids, are described. The enzyme required divalent cations for reaction, with maximal activity at 10mm Mn²⁺, and exhibited a dual optimum at pH 4–5 and pH 6 depending upon the buffer used, with the highest activity at pH 4.5 in MES buffer. This enzyme strictly recognized the Gal1-4GlcNAc terminal structure, and was highly specific for neolacto (type 2) glycolipids as acceptor. The enzyme was localized specifically in the brain, and was barely detected in other issues, including the thymus, spleen, liver, kidney, lung, and sciatic nerve fibres. Phosphatidylinositol and phosphatidylserine increased the enzymatic reaction 4.4- and 2.3-fold, respectively, whereas phosphatidylcholine slightly decreased the rate.Abbreviations GlcA glucuronic acid - Lc-PA₁₄ lactotetraose-phenyl-C₁₄H₂₉ - nLc-PA₁₄ neolactotetraose-phenyl-C₁₄H₂₉ - nLcOse₄-Cer neolactotetraosylceramide - NP-40 Nonidet P-40 - PC phosphatidylcholine - PE phosphatidylethanolamine - PI phosphatidylinositol - PS phosphatidylserine - SGGL sulfoglucuronyl glycolipid     

Integrated Human and Ecological Risk Assessment: A Case Study of Tributyltin and Triphenyltin Compounds

Tributyltin and triphenyltin (TBT and TPT) are biocides that have been used to prevent fouling of boats, preserve wood, kill molluscs, and other uses. Due to observed effects on oysters and snails, their use in boat paints has been banned in many nations. However, use on ships and some uses other than as antifouling paints continue. These uses, the relative persistence of these compounds, their tendency to bioaccumulate, and their toxicity cause lingering concerns about risks to humans and non-human organisms. This paper outlines an integrated assessment of TBT and TPT. Based on prior human health and ecological assessments, it suggests that an integrated assessment that recognized common pathways of transport, fate and exposure, and common modes of action would be more efficient and complete than additional independent assessments. The presentation of risks in an integrated manner could also lead to better decisions by defining the various benefits of any management action.     

The role of tower height and guy wires on avian collisions with communication towers

Every year an estimated 4–5 million migratory birds collide with communication towers in the United States. We examined the relative risks that tower support systems and tower height pose to migrating and other birds. We collected data comparing tower support systems (guyed vs. unguyed) and tower height categories in Michigan during 20 days of the peak of songbird migration at 6 towers in September–October 2003, 23 towers in May 2004, 24 towers in September 2004, and 6 towers in both May and September 2005. We systematically and simultaneously searched for bird carcasses under each tower and measured carcass removal and observer detection rates each season. Of those towers, 21 were between 116 and 146 m above ground level (AGL, medium) and 3 were >305 m AGL (tall). During the five 20-day sample periods we found a mean of 8.2 bird carcasses per guyed medium tower and a mean of 0.5 bird carcasses under unguyed medium towers. During four 20-day sample periods we detected a mean of 34.7 birds per guyed tall tower. Using both parametric and nonparametric tests (Mann–Whitney U-test, Kruskal–Wallis test, and Tukey's Honestly Significant Difference multiple comparison procedure) we determined that unguyed medium towers were involved in significantly fewer fatalities than guyed medium towers. We detected 54–86% fewer fatalities at guyed medium towers than at guyed tall towers. We found 16 times more fatalities at guyed medium towers than at unguyed medium towers. Tall, guyed towers were responsible for 70 times as many bird fatalities as the unguyed medium towers and nearly five times as many as guyed medium towers. These findings will provide managers and regulators, such as the US Fish and Wildlife Service, with quantitative data; thereby, allowing them to effectively work with the Federal Communications Commission in siting and authorizing tower placement. © 2011 The Wildlife Society.     

The abundance,distribution and structural characteristics of tree‐holes in Nothofagus forest,New Zealand

Tree‐holes provide an important microhabitat that is used for feeding, roosting and breeding by numerous species around the world. Yet despite their ecological importance for many of New Zealand's endangered species, few studies have investigated the abundance or distribution of tree‐holes in native forests. We used complementary ground and climbed tree surveys to determine the abundance, distribution and characteristics of tree‐holes in undisturbed Nothofagus forest in the Lewis Pass, New Zealand. We found that hole‐bearing trees were surprisingly abundant compared with many other studies, including Australian Eucalyptus species and American beech. In fact, we estimated as many as 3906 tree‐holes per hectare, of which 963 holes per hectare were potentially large enough to provide roost sites for hole‐nesting bats in New Zealand, while only eight holes per hectare were potentially suitable for specialist hole‐nesting birds. This was of great interest as primary cavity‐excavating animals are absent from New Zealand forests, compared with North America and Australia. Moreover, tree‐hole formation in New Zealand is likely to be dominated by abiotic processes, such as branch breakage from windstorms and snow damage. As has been found in many other studies, tree‐holes were not uniformly distributed throughout the forest. Tree‐holes were significantly more abundant on the least abundant tree species, Nothofagus fusca, than on either N. menziesii or N. solandri. In addition to tree species, tree size was also an important factor influencing the structural characteristics of tree‐holes and their abundance in this forest. Moreover, these trends were not fully evident without climbed tree surveys. Our results revealed that ground‐based surveys consistently underestimated the number of tree‐holes present on Nothofagus trees, and illustrate the importance of using climbed inspections where possible in tree‐hole surveys. We compare our results with other studies overseas and discuss how these are linked to the biotic and abiotic processes involved in tree‐hole formation. We consider the potential implications of our findings for New Zealand's hole‐dwelling fauna and how stand dynamics and past and future forest management practices will influence the structural characteristics of tree‐holes and their abundance in remnant forest throughout New Zealand.     

High-level 2H/13C/15N labeling of proteins for NMR studies

Summary The protein human carbonic anhydrase II (HCA II) has been isotopically labeled with ²H, ¹³C and ¹⁵N for high-resolution NMR assignment studies and pulse sequence development. To increase the sensitivity of several key ¹H/¹³C/¹⁵N triple-resonance correlation experiments, ²H has been incorporated into HCA II in order to decrease the rates of ¹³C and ¹H_N T₂ relaxation. NMR quantities of protein with essentially complete aliphatic ²H incorporation have been obtained by growth of E. coli in defined media containing D₂O, [1,2-¹³C₂, 99%] sodium acetate, and [¹⁵N, 99%] ammonium chloride. Complete aliphatic deuterium enrichment is optimal for ¹³C and ¹⁵N backbone NMR assignment studies, since the ¹³C and ¹H_N T₂ relaxation times and, therefore, sensitivity are maximized. In addition, complete aliphatic deuteration increases both resolution and sensitivity by eliminating the differential ²H isotopic shift observed for partially deuterated CH_nD_m moieties.     

Exploring the linkage between cell culture process parameters and downstream processing utilizing a plackett‐burman design for a model monoclonal antibody

Linkage of upstream cell culture with downstream processing and purification is an aspect of Quality by Design crucial for efficient and consistent production of high quality biopharmaceutical proteins. In a previous Plackett‐Burman screening study of parallel bioreactor cultures we evaluated main effects of 11 process variables, such as agitation, sparge rate, feeding regimens, dissolved oxygen set point, inoculation density, supplement addition, temperature, and pH shifts. In this follow‐up study, we observed linkages between cell culture process parameters and downstream capture chromatography performance and subsequent antibody attributes. In depth analysis of the capture chromatography purification of harvested cell culture fluid yielded significant effects of upstream process parameters on host cell protein abundance and behavior. A variety of methods were used to characterize the antibody both after purification and buffer formulation. This analysis provided insight in to the significant impacts of upstream process parameters on aggregate formation, impurities, and protein structure. This report highlights the utility of linkage studies in identifying how changes in upstream parameters can impact downstream critical quality attributes. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:163–170, 2017