bluuebunny/crossref_metadata_2025_split huggingface dataset:
History meets ecology: a geographical analysis of ecological restriction in the Neotropical humid montane forests avifaunas
Authors: Sánchez‐González Luis Antonio , Navarro‐Sigüenza Adolfo G. 
Published: October 2008

ABSTRACTAim  To analyse the ecological patterns of distribution of the avifaunas of the Neotropical humid montane forests, by assessing the degree of habitat restriction among species through the calculation of a numerical index, analysing their relationships with adjacent habitat, and exploring the relative contribution of both higher and lower habitats in shaping the avian assemblages.Location  The Neotropical humid montane forests, from Mexico to north‐western Argentina.Methods  The degree of species’ restriction to the habitat was calculated through a restriction index based on published endemicity indexes. The index scores range from 0 to 1: a score of 1 indicates a totally endemic species (i.e. fully restricted to the habitat); values tending to 0 indicate a widespread species.Results  In Mesoamerica, completely restricted species represent a lower proportion of the total avifauna than in South American humid montane forests; whereas species shared to other habitats showed a higher proportion of the avifauna with affinities to higher altitude forests (e.g. pine and pine‐oak forests). South America, on the other hand, holds assemblages with a high proportion of completely restricted species; species shared to other habitats showed a high proportion of taxa with affinities to lowland forests.Main conclusions  The ecological distribution of the HMF's avifauna could be partitioned in three main components: the ecologically restricted avifauna, the high altitude species and, the lower altitude species, which are tightly associated to the floristic composition along the gradient. The history of formation of the HMF flora and the ecological distribution of different avian taxa suggest a common history. Finally, the restriction index allowed a detailed evaluation of the composition of avian assemblages, their degree of restriction to the habitat and of the affinities regarding adjacent habitats, as well as an accurate distinction between species richness and restricted species richness, which should be a fundamental step towards the establishment of conservation priorities.
Indicator taxa revisited: useful for conservation planning?
Authors: Larsen Frank Wugt , Bladt Jesper , Rahbek Carsten 
Published: October 2008

ABSTRACTAim  Indicators for biodiversity are needed to facilitate the identification of complementary reserve networks for biodiversity conservation. One widely adopted approach is to use indicator taxa, i.e. a single taxon such as birds or butterflies, despite the ongoing debate regarding their usefulness as indicators of broader biodiversity. Here we assess several aspects, such as influence of species number, of indicator taxa for three extensive data sets to improve our insight into the effectiveness of indicator taxa.Location  Denmark, sub‐Saharan Africa and Uganda.Methods  First, we investigate to what extent variation in species number between indicator taxa (e.g. 488 mammal spp. vs. 210 snake spp.) is causing the differences in effectiveness between indicator taxa. Second, we investigate whether indicator taxa are capable of outperforming indicator groups composed of random sets of species chosen among all taxa. Finally, we assess the correlation of specific properties such as mean range size of the indicator taxa to their effectiveness. We investigate these aspects of the effectiveness of indicator taxa through the separate analysis of three distinct distributional species data sets: sub‐Saharan Africa (4,039 spp.), Denmark (847 spp.) and Uganda (2,822 spp.).Results  We overall found that indicator taxa comprising a greater number of species tend to perform better than indicator taxa with fewer species (e.g. 488 mammal spp. outperform 210 snake spp.), although there are some exceptions. Second, we found most indicator taxa to perform worse than indicator groups consisting of a comparable number of species selected among all taxa. Finally, the effectiveness of indicator taxa was seen to correlate poorly with selected distributional properties such as mean range size of the indicator taxa, suggesting that it is difficult to predict which taxa are efficient biodiversity indicators.Main conclusions  Overall, these findings might suggest that focus should simply be on increasing the number of species among all taxa as basis for priority setting, rather than striving to obtain the ‘perfect’ indicator taxa.
Conservation of Neotropical carnivores under different prioritization scenarios: mapping species traits to minimize conservation conflicts
Authors: Loyola Rafael D. , De Oliveira Guilherme , Diniz‐Filho José Alexandre Felizola , Lewinsohn Thomas M. 
Published: October 2008

ABSTRACTAim To define priority sets of ecoregions that should be sufficiently covered in a reserve system to represent all Neotropical carnivores (Mammalia: Carnivora) under three distinct conservation scenarios.Location The Neotropical region.Methods We used broad‐scale biogeographical data of species distribution to define priority sets of ecoregions for conservation of carnivores and mapped four species traits (phylogenetic diversity, body size, rarity and extinction risk), which were used as constraints in prioritization analyses, based on the complementarity concept. We proposed three scenarios: a very vulnerable one, one of species persistence and another of lower human impact. We used the simulated annealing algorithm to generate ecoregion‐irreplaceability pattern and to find the combinations of ecoregions in each conservation scenario.Results We found that only 8% of Neotropical ecoregions are needed to represent all 64 carnivore species at least once. Rain forest ecoregions harbour a greater amount of carnivore phylogenetic diversity, whereas the tropical Andes hold large‐bodied carnivores. Western and southern Neotropical ecoregions have more rare species as well as higher threat levels. In the lower human‐impact set, 12 ecoregions were needed to represent all species. These coincide only partially with those attained by other prioritization scenarios. In the very vulnerable and in the species persistence scenario, 14 and 12 ecoregions were represented, respectively, and the congruence between either one and the lower human‐impact set was fairly low. Shared ecoregions are located in Mexico, Costa Rica, northern Amazon and western Chile.Main conclusions Our results highlight areas of particular interest for the conservation of Neotropical carnivores. The inclusion of evolutionary and ecological traits in conservation assessments and planning helps to improve reserve networks and therefore to increase the effectiveness of proposed priority sets. We suggest that conservation action in the highlighted areas is likely to yield the best return of investments at the ecoregion scale.
Gap analysis: a tool for complementary genetic conservation assessment
Authors: Maxted Nigel , Dulloo Ehsan , V Ford‐Lloyd Brian , Iriondo Jose M. , Jarvis Andy 
Published: October 2008

ABSTRACTAim  Gap analysis is a well‐established conservation technique that identifies areas in which selected elements of biodiversity are represented and through comparison with existing in situ protected area networks identifies habitats or ecosystems that need additional protection. We aim to demonstrate that gap analysis may be extended to encompass both in situ and ex situ genetic diversity conservation strategies.Location  Global, with exemplar case study from sub‐Saharan Africa.Methods  An extended methodology of gap analysis is proposed that involves the following steps: (1) circumscription of target taxon and target area; (2) assessment of natural diversity through a review of intrinsic taxonomic, genetic and ecogeographical diversity combined with threat assessment; (3) assessment of current complementary in situ and ex situ conservation strategies; and (4) reformulation of the conservation strategy through analysis of the differences between the pattern of natural, intrinsic diversity and the elements of that diversity already effectively represented by existing in situ and ex situ conservation actions.Results  To illustrate the gap analysis approach proposed, the methodology was applied to the conservation of African Vigna species (cowpea Vigna unguiculata (L.) Walp. and its wild relatives) and indicated: (1) genetic reserves should be established at the southern tip of Lake Tanganyika, the coastal area of Sierra Leone and between Lake Victoria and the other Great Lakes, and (2) 14 taxa and several countries should be targeted for further seed collection.Main conclusions  The robust nature of the extended methodology for gap analysis has been demonstrated and indicates that its scope as an effective conservation tool may be expanded to fully address the need for a more comprehensive and complementary conservation strategy that encompasses both in situ and ex situ applications. However, it should be stressed that the methodology is applicable for any form of biodiversity (wild or cultivated), where the conservation of genetic diversity is the prime goal.
Smaller and more numerous harvesting gaps emulate natural forest disturbances: a biodiversity test case using rove beetles (Coleoptera, Staphylinidae)
Authors: Klimaszewski Jan , Langor David W. , Work Timothy T. , Hammond James H.E. , Savard Karine 
Published: October 2008

ABSTRACTAim  To evaluate changes in the abundance, species richness and community composition of rove beetles (Coleoptera, Staphylinidae) in response to three configurations of experimental gap cuts and to the effects of ground scarification in early succession yellow birch‐dominated boreal forest. In each experimental treatment, total forest removed was held constant (35% removal by partial cutting with a concomitant decrease in gap size) but the total number of gaps was increased (two, four and eight gaps, respectively), resulting in an experimental increase in the total amount of ‘edge’ within each stand.Location  Early succession yellow birch‐dominated forests, Quebec, Canada.Methods  Pitfall traps, ANOVA, MIXED procedure in sas®, post hoc Tukey's adjustment, rarefaction estimates, sum‐of‐squares and distance‐based multivariate regression trees (ssMRT, dbMRT).Results  Estimates of species richness using rarefaction were highest in clearcut and two‐gap treatments, decreased in smaller and more numerous gaps and were significantly higher in scarified areas than in unscarified areas. ANOVA indicated a significant impact of harvesting on the overall standardized catch. Post hoc Tukey's tests indicated that the total catch of all rove beetles was significantly higher in uncut forests than in the treated areas. Both sum‐of‐squares and distance‐based multivariate regression trees indicated that community structure of rove beetles differed among treatments. Assemblages were grouped into (a) control plots, (b) four‐ and eight‐gap treatments and (c) two‐gap and clearcut treatments.Main conclusions  Rove beetle composition responded significantly to increasing gap size. Composition among intermediate and small‐sized gap treatments (four‐ and eight‐gap treatments) was more similar to uncut control forests than were larger gap treatments (two‐gap) and clearcuts. Effects of scarification were nested within the harvested treatments. When the total area of forest removed is held constant, smaller, more numerous gaps are more similar to uncut control stands than to larger gaps and falls more closely within the natural forest heterogeneity.
Herbivory is related to taxonomic isolation, but not to invasiveness of tropical alien plants
Authors: Dawson Wayne , Burslem David F. R. P. , Hulme Philip E. 
Published: October 2008

ABSTRACTAim  The enemy release hypothesis is often invoked to explain why some alien plant species become invasive. Here, we investigated relationships between invasiveness, taxonomic isolation and leaf herbivory for tropical alien plant species introduced to a botanical garden in East Africa.Location  Amani Botanical Garden, East Usambara mountains, northeast Tanzania.Methods  We measured the proportion of leaves damaged, and the percentage leaf area damaged on individuals of 28 alien plant species. We extracted data on the presence/absence of native congeners and the number of native confamilial species from an inventory of the East Usambara flora. We also obtained data on planting effort for 26 species, from historical records. Linear and generalized linear models were used to analyse the relationships between invasiveness, herbivory and taxonomic isolation.Results  Mean proportion of leaves damaged per species was significantly explained by taxonomic isolation; proportion of leaves damaged increased with the number of native confamilial species and was greater, on average, for species with native congeners than those without native congeners. The mean percentage of leaf area damaged per species could not be explained by any variables considered in this study. There was no relationship between the degree of herbivory or taxonomic isolation and alien plant species invasiveness, but more‐invasive species did have a significantly greater planting effort than less‐invasive species.Conclusions  The role herbivores play in controlling alien plant invasions has been investigated relatively little in the tropics. In this study, although the amount of herbivory suffered by alien plants was related to taxonomic isolation, we found no evidence for leaf‐feeding invertebrates having a significant role in invasion, suggesting that other factors may be responsible for differences in species success.
Computer‐assisted simulations of phosphofructokinase‐1 kinetics using simplified velocity equations
Authors: Roy Harry , Diwan Joyce , D. Segel Leigh , Segel Irwin H. 
Published: October 2008

AbstractEquations useful for simulating the kinetic behavior of phosphofructokinase are presented. The equations, which are based on the concerted transition (symmetry) model for allosteric enzymes, account for substrate inhibition by MgATP, cooperative binding by F‐6‐P, activation by F‐2, 6‐P2, and deinhibition by AMP. Velocity calculations can be performed using either a spreadsheet program (e.g., MS Excel) or a web‐based program (e.g., Authorware). Both approaches are illustrated. © 2001 IUBMB. Published by Elsevier Science Ltd. All rights reserved.
Developing experimental design and troubleshooting skills in an advanced biochemistry lab
Authors: Roberts Linda M. 
Published: October 2008

AbstractTwo skills critically important to all scientists are the ability to design good experiments and to troubleshoot experiments that do not yield the expected results. In spite of their importance, however, these skills are rarely taught as a part of the undergraduate science curriculum. This deficiency was addressed by creating an advanced biochemistry laboratory course that focuses on the development of experimental design and troubleshooting skills. The course provides students with the opportunity to design and evaluate their own experiments through semester‐long independent projects that have a common theme (in this case, protein purification, but any theme could be used). Students plan their projects and carry through the experiments by consulting the primary research literature. The instructor provides minimal input in troubleshooting situations, instead allowing the student to think through and implement alternative solutions. A 2‐year survey of the course revealed that students were often frustrated but felt the course significantly improved their experimental laboratory skills as well as introducing them to “real‐world” laboratory experience. They further indicated that they preferred the approach used in this course to directed “cook‐book” laboratory experiences. © 2001 IUBMB. Published by Elsevier Science Ltd. All rights reserved.
Structural determinants of mini‐protein stability
Authors: Polticelli Fabio , Raybaudi‐Massilia Gabriella , Ascenzi Paolo 
Published: October 2008

AbstractMini‐proteins can be defined as polypeptides shorter than 40–50 residues which nevertheless exhibit a well defined tertiary structure. Mini‐proteins represent simple and useful model systems to study the structural determinants of protein folding and stability and to illustrate such principles within biochemistry and molecular biology educational context. Here, strategies adopted by different classes of mini‐proteins to attain family‐characteristic, well‐ordered, three‐dimensional structures are reviewed. © 2001 IUBMB. Published by Elsevier Science Ltd. All rights reserved.
Water: its importance to life
Authors: Chaplin Martin F. 
Published: October 2008

AbstractTextbooks increasingly include material concerning the importance of water but this topic is often treated over‐simplistically with insufficient attention being given to the central position of water in life processes. In this article, modern views of the fundamental role that water plays in biochemical function and process are summarized. The importance of water in the structures of nucleic acids and proteins is explained. © 2001 IUBMB. Published by Elsevier Science Ltd. All rights reserved.
Analysis of the tetranucleotide polymorphic HUMTH01 microsatellite
Authors: Lajoie‐Mazenc Isabelle , Couderc Bettina 
Published: October 2008

AbstractThe major aim of this practical class in molecular biology is to familiarize students with some common manipulations of DNA (extraction from buccal swabs, electrophoresis, etc.) and to allow them to carry out the polymerase chain reaction, on their own DNA, in order to amplify a sequence containing a tetranucleotide microsatellite (HUMTH01). This class is also providing experience in DNA finger printing by comparing the size of the sequences amplified from each student's DNA. These sequences correspond to tetranucleotide microsatellite polymorphisms. © 2001 IUBMB. Published by Elsevier Science Ltd. All rights reserved.
Using a classical method of vitamin C quantification as a tool for discussion of its role in the body
Authors: Ciancaglini. Pietro , Santos Hérica L. , Daghastanli Katia R. P. , Jr. Geraldo Thedei 
Published: October 2008

AbstractThe main objective of this experiment is to determine the amount of vitamin C present in fruits, beverages or vitamin C tablets, by performing titrations and the necessary calculations.Dilferent methods are available for this determination but the titration method is proposed as the simplest and low cost experimental procedure that gives an approximate result to the student and allows calculation of the vitamin C amount.Once the vitamin C in foodstuffs is quantified, students are guided to compare their results to the recommended daily allowance. This leads to discussion about fruits and fresh green vegetables consumption in the human daily diet needs, not only of vitamin C, but also β‐carotene and others. © 2001 IUBMB. Published by Elsevier Science Ltd. All rights reserved.
Truncated hemoglobins: trimming the classical ‘three‐over‐three’ globin fold to a minimal size
Authors: Milani Mario , Pesce Alessandra , Bolognesia Martino , Ascenzi Paolo 
Published: October 2008

AbstractTruncated hemoglobins (trHbs) host the heme in a ‘two‐over‐two’ α‐helical sandwich which results from extensive editing of the classical ‘three‐over‐three’ globin fold. The three‐dimensional structure of trHbs is based on four main α‐helices, arranged in a sort of α‐helical bundle composed of two antiparallel helix pairs (B/E and G/H). Most notably, trHbs deviate from the conventional globin fold in that they display an extended loop substituting for the heme proximal F‐helix observed in globins. Moreover, since efficient adaptation of a 110–130 amino acid trHb chain to host the porphyrin ring firstly requires specific chain flexibility, trHbs contain three invariant Gly‐based motifs. Inspection of the trHb three‐dimensional trHb structures shows that an apparent protein cavity or tunnel would connect the protein surface to an inner region very close to the heme distal site. Such a structural feature, never observed before in (non) vertebrate globins, may have substantial implications for ligand diffusion and binding properties in trHbs. © 2001 IUBMB. Published by Elsevier Science Ltd. All rights reserved.
Article Myoglobin: a pseudo‐enzymatic scavenger of nitric oxide
Authors: Ascenzi Paolo , Brunori Maurizio 
Published: October 2008

AbstractMyoglobin (Mb) is reported in biochemistry and physiology textbooks to act as an O2 reservoir and to facilitate O2 diffusion from capillaries to mitochondria, to sustain cellular respiration. Recently, it has been proposed that Mb is an intracellular scavenger of bioactive nitric oxide (NO), regulating its level in the skeletal and cardiac muscle and thereby protecting mitochondrial respiration, which is impaired by NO. This novel function of Mb is based on the rapid and irreversible reaction of ferrous oxygenated Mb (MbO2) with NO yielding ferric oxidized Mb (metMb) and nitrate (NO3). The efficiency of this process, which is postulated to depend on the superoxide (O2) character acquired by O2 once bound to the heme iron, may be enhanced by intramolecular diffusion of NO trapped momentarily into cavities of the protein matrix. O2 can also react with ferrous nitrosylated Mb (MbNO), albeit very slowly, leading to metMb and NO3. The O2‐dependent NO‐detoxification process may be considered to be pseudo‐enzymatic given that metMb obtained by the primary reaction of MbO2 with NO is reduced back to ferrous Mb by a specific metMb‐reductase, and can therefore repeat a cycle of NO conversion to harmless nitrate. © 2001 IUBMB. Published by Elsevier Science Ltd. All rights reserved.
Article Revision bingo
Authors: Willmott Chris J. R. 
Published: October 2008

AbstractBingo can be a versatile and engaging tool for spicing up end‐of‐module revision and other contexts in which course content is being reviewed. Instead of numbers being called out, students are given a verbal clue that fits with one of the answers on their playing grid. Get five correct answers in any straight line (including either of the major diagonals) and they win the game. The interactive and light‐hearted medium of a bingo game can provide motivation for study and enhance learning by the students. Protein revision bingo is included as an example. © 2001 IUBMB. Published by Elsevier Science Ltd. All rights reserved.
Aminotransferase from insect cells
Authors: Erwin Hilary , de Ridder Grace , Barton Peter A 
Published: October 2008

AbstractThe presence of transaminase activity is demonstrated in the cultured insect cell line Sf21 (Spodoptera frugiperda) at a level sufficient to enable replacement of rat liver in an undergraduate student experiment designed to demonstrate enzyme activity responsible for amino acid interconversions. © 2001 Published by Elsevier Science Ltd. on behalf of IUBMB.
The Sarbanes‐Oxley Act of 2002 and Market Liquidity
Authors: Jain Pankaj K. , Kim Jang‐Chul , Rezaee Zabihollah 
Published: October 2008

AbstractInvestors rely heavily on the trustworthiness and accuracy of corporate information to provide liquidity to the capital markets. We find that the rash of financial scandals caused a severe deterioration in market liquidity in the form of wider spreads, lower depths, and a higher adverse selection component of spreads vis‐à‐vis their benchmark levels. Regulatory responses including the Sarbanes‐Oxley Act of 2002 (SOX) had inconsequential short‐term liquidity effects but highly significant and positive long‐term liquidity effects. These liquidity improvements are positively associated with the improved quality of financial reports, several firm‐specific variables (e.g., size), and market factors (e.g., price, volatility, volume).