Are BOLD searches scientific? A response to Federhen (2011)

In 2011 Waugh et al. presented the results of a DNA barcoding study that identified avian species involved in birdstrikes. Federhen (2011) criticised this study by suggesting that some of the sequences on which identifications were based were not publicly available because access to them in the Barcode of Life database was restricted. Hence, according to Federhen (2011) the study is not repeatable. We disagree and discuss the role of databases in DNA barcoding generally.     

Birdstrikes and barcoding: can DNA methods help make the airways safer?

While flying remains one of the safest means of travel, reported birdstrikes on aircraft have risen. This is a result of increased aircraft flight movements, changes in agricultural methods and greater environmental awareness contributing to growing populations of hazardous bird species, as well as more diligent reporting of incidents. Measures to mitigate this hazard require accurate data about the species involved; however, the remains of birds from these incidents are often not easy to identify. Reported birdstrikes include a substantial number where the species cannot be determined from morphology alone. DNA barcoding offers a reliable method of identifying species from very small amounts of organic material such as blood, muscle and feathers. We compare species identification based on morphological criteria and identifications based on mitochondrial cytochrome c oxidase subunit I DNA barcoding methods for New Zealand species. Our data suggest that DNA-based identification can substantially add to the accuracy of species identifications, and these methods represent an important addition to existing procedures to improve air safety. In addition, we outline simple and effective protocols for the recovery and processing of samples for DNA barcoding.     

An ecological approach to birdstrike risk analysis

Airports are peculiar developed habitats that, besides being extremely noisy and unappealing to some bird species, are highly attractive to others. Bird–aircraft collisions, or birdstrikes, cause losses in terms of human lives, direct monetary losses and associated costs for the civil aviation industry. In recent years, birdstrike risk assessment studies have focused on the economical aspects of the damage caused by wild animals and the hazards of wildlife–aircraft collisions, while an ecological approach, taking into account animal behaviour for the analysis of such events, has seldom been adopted. We conducted a risk analysis for birdstrikes at the Venice Marco Polo International Airport (VCE), Italy. We defined the key variables involved in these events and summarised their interactions in a single metric risk index we called the “Birdstrike Risk Index” (BRI). Our aim was to provide a tool for birdstrike risk analysis that described the risk on the basis of the actual presence of birds at airports. The application of the BRI at VCE allows relative risks across species to be defined, providing information for prioritising management actions. Furthermore, due to the seasonality of bird species presences, the application of the BRI to a long-term data series should give clues of birdstrike risk in future scenarios. This new ecological approach that we applied to a particular airport could easily be adapted for use at other airports worldwide and integrated into risk assessment procedures. The study results and the BRI tool are addressed to scientific consultants of airport safety managers.     

Ranking birdstrike risk: A case study at Huanghua International Airport, Changsha, China

Bird-aircraft collisions (birdstrikes) pose a major threat to aviation safety worldwide. The bird distribution at the airfield of Huanghua International Airport in Changsha, Hunan Province, China, was investigated between December of 2006 and December of 2008, to study birdstrike avoidance and aviation safety. A total of 60 bird species was found and their risks were assessed by a birdstrike ranking assessment system. The highest-risk species were Barn swallow (Hirundo rustica), Red-rumped swallow (H. daurica), Grey-headed lapwing (Vanellus cinereus), Pintail snipe (Gallinago stenura), Oriental skylark (Alauda gulgula), Little egret (Egretta garzetta), and Eurasian woodcock (Scolopax rusticola), whereas the lowest-risk species were Black-capped kingfisher (Halcyon pileata) and White-throated kingfisher (H. smyrnensis). Through a hierarchical cluster analysis, all species were classified as four groups: (1) the extremely high-risk group with a risk level between 84% and 100%, which includes bird species ranked from the 1st to the 16th, and is the priori group in birdstrike prevention; (2) the high-risk group with a risk level between 71% and 81%, which includes bird species ranked from the 17th to the 28th, and is the sub-prior group in birdstrikes; (3) the sub-high-risk group with a risk level between 60% and 69%, which includes bird species ranked from the 29th to the 43rd, and is the concern group in birdstrike prevention; (4) the low-risk group with a risk level between 60% and 69%, which includes bird species ranked from the 44th to the 60th, and is the negligible group in birdstrike prevention. Finally, the first 16 bird species with high-risk values, which are the main focus of birdstrike prevention, were categorized as six prevention groups by a hierarchical cluster analysis. Therefore, this study provides targeted implementations for birdstrike prevention at Huanghua International Airport, Changsha.     

Ranking birdstrike risk: A case study at Huanghua International Airport, Changsha, China

Bird-aircraft collisions (birdstrikes) pose a major threat to aviation safety worldwide. The bird distribution at the airfield of Huanghua International Airport in Changsha, Hunan Province, China, was investigated between December of 2006 and December of 2008, to study birdstrike avoidance and aviation safety. A total of 60 bird species was found and their risks were assessed by a birdstrike ranking assessment system. The highest-risk species were Barn swallow (Hirundo rustica), Red-rumped swallow (H. daurica), Grey-headed lapwing (Vanellus cinereus), Pintail snipe (Gallinago stenura), Oriental skylark (Alauda gulgula), Little egret (Egretta garzetta), and Eurasian woodcock (Scolopax rusticola), whereas the lowest-risk species were Black-capped kingfisher (Halcyon pileata) and White-throated kingfisher (H. smyrnensis). Through a hierarchical cluster analysis, all species were classified as four groups: (1) the extremely high-risk group with a risk level between 84% and 100%, which includes bird species ranked from the 1st to the 16th, and is the priori group in birdstrike prevention; (2) the high-risk group with a risk level between 71% and 81%, which includes bird species ranked from the 17th to the 28th, and is the sub-prior group in birdstrikes; (3) the sub-high-risk group with a risk level between 60% and 69%, which includes bird species ranked from the 29th to the 43rd, and is the concern group in birdstrike prevention; (4) the low-risk group with a risk level between 60% and 69%, which includes bird species ranked from the 44th to the 60th, and is the negligible group in birdstrike prevention. Finally, the first 16 bird species with high-risk values, which are the main focus of birdstrike prevention, were categorized as six prevention groups by a hierarchical cluster analysis. Therefore, this study provides targeted implementations for birdstrike prevention at Huanghua International Airport, Changsha.     

A Land-Use Perspective for Birdstrike Risk Assessment: The Attraction Risk Index

Collisions between aircraft and birds, birdstrikes, pose a serious threat to aviation safety. The occurrence of these events is influenced by land-uses in the surroundings of airports. Airports located in the same region might have different trends for birdstrike risk, due to differences in the surrounding habitats. Here we developed a quantitative tool that assesses the risk of birdstrike based on the habitats within a 13-km buffer from the airport. For this purpose, we developed Generalized Linear Models (GLMs) with binomial distribution to estimate the contribution of habitats to wildlife use of the study area, depending on season. These GLMs predictions were combined to the flight altitude of birds within the 13-km buffer, the airport traffic pattern and the severity indices associated with impacts. Our approach was developed at Venice Marco Polo International airport (VCE), located in northeast Italy and then tested at Treviso Antonio Canova International airport (TSF), which is 20 km inland. Results from the two airports revealed that both the surrounding habitats and the season had a significant influence to the pattern of risk. With regard to VCE, agricultural fields, wetlands and urban areas contributed most to the presence of birds in the study area. Furthermore, the key role of distance of land-uses from the airport on the probability of presence of birds was highlighted. The reliability of developed risk index was demonstrated since at VCE it was significantly correlated with bird strike rate. This study emphasizes the importance of the territory near airports and the wildlife use of its habitats, as factors in need of consideration for birdstrike risk assessment procedures. Information on the contribution of habitats in attracting birds, depending on season, can be used by airport managers and local authorities to plan specific interventions in the study area in order to lower the risk.     

Using DNA barcodes to identify a bird involved in a birdstrike at a Chinese airport

One day at dusk in August, 200X, an airplane was struck by a bird at a Chinese airport (M Airport). After a careful check, some blades of the plane’s engine were found to be out of shape and a few feathers and some bloodstains were found in the air intake of the engine. In order to know which species of bird was involved in the birdstrike, firstly we extracted DNA from the bloodstains; secondly, the DNA barcode (portion of COI gene) of the unknown species was amplified by PCR method; thirdly, sequence divergences (K2P differences) of the DNA barcode between the unknown species and a library of 59 common bird species distributed at the airport area were analyzed. Furthermore, a neighbor-joining (NJ) tree based on COI barcodes was created to provide graphic representation of sequence divergences among the species to confirm the identification. The result showed that red-rumped swallow (Hirundo daurica) was involved in the birdstrike incident. Some suggestions to avoid birdstrikes caused by red-rumped swallows were given to the administrative department of M Airport to ensure flying safety.     

Estimation of the evolutionary stability of the Influenza A virus: Prediction of variable regions in the domain structure of the M1 protein

Influenza virus is a human pathogen that is responsible for several pandemics with high death rates. Two programs were written for the statistical analysis of the coding regions of genes from extensive samples of Influenza A virus. While inner viral proteins appeared to be evolutionarily stable, surface antigens and the NS1 nonstructural protein are highly variable. Using programs to predict the evolutionarily variable regions inside the M1 protein sequence it was shown that the N-domain is the most conserved domain while the M- and C-domains are the most variable. In addition, the C-domain was shown to be the most unfolded one, according to prediction by the DISOPRED algorithm and, thus, possesses the most structural plasticity.     

Chemotherapy of small cell lung cancer

The author summarizes the most recent information on small cell lung cancer. Reviews the epidemiology, prognostic markers and stages of small cell lung cancer Details the more frequently used combined therapeutic modalities, the criteria of the optimal therapeutic approaches and the achieved remission rates. Based on the most recent data, summarizes the new chemotherapeutic agents and their most effective combinations, the second line treatment and immunotherapy. Finally tries to answer the most frequently asked questions.     

Rarity, commonness, and patterns of species richness: the mammals of Mexico

Aim To determine whether rare or common species contribute most to overall patterns of spatial variation in extant species richness. Location Mexico. Methods Using data on the distribution of mammal species across Mexico at a quarter degree resolution, we ranked species from the most widespread to the most restricted (common‐to‐rare) within the study area, and from the most restricted to the most widespread (rare‐to‐common), and generated a sequence of patterns of species richness for increasing numbers of species. At each stage along both series of richness patterns, we correlated the species richness pattern for the subassemblage with that of the full assemblage. This allows comparison of subassemblages of the n most common with the n most rare species, in terms of how well they match the full assemblage richness pattern. Further analyses examined the effects on these patterns of correlation of the amount of raw information contained in the distributions of given numbers of rare and common species. Results For the mammals of Mexico the more widely distributed species contribute disproportionately to patterns of species richness compared with more restricted species, particularly for non‐volant species and endemic species. This is not simply a consequence of differences in the volumes of information contained in the distributions of rare and common species, with the disproportionate contribution of common species if anything being sharpened when these differences are taken into account. The pattern is most clearly demonstrated by endemic species, suggesting that the contribution of common species is clearest when the causes of rarity and commonness are limited to those genuinely resulting in narrow and widespread geographical ranges, respectively, rather than artificial (e.g. geopolitical) boundaries to the extents of study regions. Conclusions Perhaps surprisingly, an understanding of the determinants of overall patterns of species richness may gain most from consideration of why common species occur in some areas and are absent from others, rather than consideration of the distributions of rare species.     

Chemical induction of presumed dominant-lethal mutations in postcopulation germ cells and zygotes of mice. II. Sensitivity of different postcopulation-precleavage stages to three alkylating chemicals.

The relative sensitivities of various postcopulation-precleabage and pronuclear stages to dominant-lethal effects of isopropyl methanesulfonate (IMS), ethyl methanesulfonate (EMS), and triethylenemelamine (TEM) were investigated. The pattern of sensitivity differed with the chemical. IMS was most effective when pronuclear formation was already completed and the majority of the zygotes were presumably undergoing DNA synthesis. EMS, on the other hand, induced its most pronounced effects when eggs in the course of second meiotic division and zygotes in early pronuclear stages were treated. The greatest effect of TEM was observed when zygotes were treated at the early pronuclear stage. EMS and TEM, in contrast to IMS, are similar to radiations in that zygotes undergoing DNA synthesis are more resistant to them than are the early pronuclear stages. In the case of IMS, effects induced in the most sensitive postcopulation-precleavage stage were 6 to 9 times greater than in the most sensitive precopulatory dictyate oocytes or male germ cells. On the other hand, in the case of EMS and TEM, the most sensitive precopulatory male germ cells, but not the dictyate oocytes, were more sensitive than the most sensitive postcopulation stages.     

不同风信子品种在南京地区的物候期及生长特性分析

对从荷兰引进的17个风信子(Hyacinthus orientalis L. )品种在南京地区的物候期、观赏特性和生长状况进行了调查分析.调查结果表明,17个风信子品种的耐寒性较强,出苗期最早在1月下旬,多数品种的出苗期在2月中下旬;绝大多数风信子品种的叶片展开期集中在3月14日至20日;花现色期多为2月底至3月初,第1朵花的开花期在3月中上旬;大部分品种的单花序开花持续时间和群体开花持续时间较长,分别达20～22 d和27～31 d.17个风信子品种的花均具有非常浓烈的香味,花蕾与花脉颜色相同,花色从花脉辐射至花瓣边缘并逐渐变淡,花色艳丽, 观赏性强. 少数品种具1个花枝, 多数品种具2个花枝, 花茎长度12.7～21.9 cm, 多数品种的花茎长度在17 cm以上;主花序长度多在11 cm以上,约占整个花茎长度的2/3;单花序花朵数为20～61.各品种的花瓣数和花药数基本一致,多以6为基数;17个风信子品种的花粉均有一定的萌发能力,其中9个品种的花粉萌发率较高,均超过40%.多数品种的叶片数为6或7,叶片长18～29 cm,宽2.2～3.6 cm.除品种'阿姆斯特丹'、'简波斯'和'福特'外,其余品种均可以分生出籽球,其中,品种'蓝星'、'蓝夹克'和'爱丽斯'的籽球分生能力最强,分生率达66%以上;不同风信子品种的籽球直径也各不相同,多数籽球直径较大,为3～5 cm.结果显示,风信子可作为早春花卉在南京进行种植,但具体种植条件尚待深入研究.     

Response of Six Strains of Eimeria brunetti to Two Antagonists of para-Aminobenzoic Acid

SYNOPSIS. Sulfaquinoxaline and ethopabate are 2 chemically distinct types of antagonist of PABA with anticoccidial action. Reversal experiments with PABA and synergism studies with pyrimethamine indicated that both compounds interfered with the PABA-folic acid metabolic sequence. Six pure strains of Eimeria brunetti responded differently to the 2 compounds. The strain most sensitive to ethopabate was one of 2 strains most resistant to sulfaquinoxaline. Conversely, the strain most sensitive to sulfaquinoxaline was unresponsive to the highest doses of ethopabate employed. Hypotheses to explain the differences in biological effects of the 2 compounds were considered.     

Choice of area for assessment

Multiple areas for assessment of skeletal maturity of an individual (hand, foot, knee, elbow, shoulder, hip) provide the broadest basis for accurate appraisal. Such studies are becoming progressively less feasible because: (1) the amount of radiation exposure involved may not be permitted; and (2) the greater time, expense and technical assistance required may not be justified by the knowledge yielded. For most statistical series it is desirable today to limit radiographs to one area. The left hand, including lower forearm, would seem the area of choice. It is most convenient, permits maximum subjects cooperation, is cheapest, most rapidly done, and may be repeated most often without objection. Uniformity and clarity of radiograms are also easiest to obtain. Standardization of techniques for use with both fixed and portable machines by widely separated workers is most readily attained. For special purposes the choice of area must be determined by the information sought. Special measures will often have to be devised to answer the questions being investigated.     

Comparison of three inbred lines of mice by overall and genetic radiosensitivity

The radiosensitivities of three mouse strains (BALB/cLacY, C3H/SnY, and 101/HY) have been compared using the following parameters: survival after irradiation at a dose of 6-7 Gy, chromosome aberration frequency in bone marrow cells after irradiation at a dose of 1.5 Gy, and the change in testis weight and frequency of abnormal sperm heads (ASHs) after irradiation at doses from 0.5 to 4 Gy. Strain BALB/c is the most radiosensitive with respect to the survival and chromosome aberration frequency in the bone marrow but the most resistant with respect to the change in testis weight and the frequency of abnormal sperm heads. Strain 101/HY was the most resistant with respect to survival and chromosome aberration frequency in bone marrow after irradiation but the most radiosensitive with respect to testis damage.     

Preliminary studies on the ability of plant barriers to capture lead and cadmium of vehicular origin

The purpose of this study is to determine the type of plant barrier most suitable for the protection of areas adjacent to roadways from the emissions of motor vehicles, as well as to establish the most efficient plant species for use in the barriers. The survey gathered the following samples: (a) grass and soil samples near the major Italian motorway networks and from sites directly exposed to vehicle emissions or protected by plant barriers; (b) samples of leaves from various species of trees, growing both alongside motorways and in urban and remote sites. The results show that the most efficient barriers are those placed immediately alongside the road edge and the most efficient species are deciduous broadleaves and small-needle conifers.     

The relationship between homozygosity and the frequency of the most frequent allele

Homozygosity is a commonly used summary of allele-frequency distributions at polymorphic loci. Because high-frequency alleles contribute disproportionately to the homozygosity of a locus, it often occurs that most homozygotes are homozygous for the most frequent allele. To assess the relationship between homozygosity and the highest allele frequency at a locus, for a given homozygosity value, we determine the lower and upper bounds on the frequency of the most frequent allele. These bounds suggest tight constraints on the frequency of the most frequent allele as a function of homozygosity, differing by at most 14 and having an average difference of 23 - pi(2)/18 approximately 0.1184. The close connection between homozygosity and the frequency of the most frequent allele-which we illustrate using allele frequencies from human populations-has the consequence that when one of these two quantities is known, considerable information is available about the other quantity. This relationship also explains the similar performance of statistical tests of population-genetic models that rely on homozygosity and those that rely on the frequency of the most frequent allele, and it provides a basis for understanding the utility of extended homozygosity statistics in identifying haplotypes that have been elevated to high frequency as a result of positive selection.     

Biological Activities of Analogues of Ser-Val-Gly-Glu (AS-I), a Toxin Pathogenic to Sunflower

The tetrapeptides Ser-Val-Glu-Gly, Hse-Val-Gly-Glu, Thr-Val-Gly-Glu, Val-Ser-Gly-Glu and Ser-Val-Glu-Gly, analogues of the AS-1 toxin which is pathogenic to sunflower, were examined for biological activity on sunflower and eight other plant species. These peptides were synthesized in solution or on a solid phase. Of the species studied by leaf inoculation, sunflower and zucchini were the most susceptible and cotton the most resistant to ail of the toxins tested. The effect of Ser-Val-Glu-Gly was similar to that reported for AS-I, whereas the tetrapeptide Thr-Val-Gly-Glu was the most toxic.     

Community structure of the deep sea fishes in the northern Gulf of Aqaba,Red Sea (Osteichthyes and Chondrichthyes)

The aim of this study was to investigate the community structure of deep sea fishes in the northern Gulf of Aqaba. Deep fish traps, short lines and long lines were deployed at depth ranges from 60 to 700 m between June 2014 and May 2015. A total of 369 fish individuals belonging to 37 species in 21 families were collected. The most abundant family observed in deep fish traps and short line was the commercially important family Sparidae, whereas the most abundant family in long line catch was the commercially unimportant fish family Muraenidae. The most abundant fish species sampled by deep fish traps and shortline was Blueskin Seabream, Polysteganus coeruleopunctatus. The most abundant species in long line catch White-spotted Moray, Gymnothorax johnsoni. In fish traps and with short line, the most commonly caught species was Blueskin Seabream. White-spotted Moray was the most common long line catch. Depth distribution for 37 deep fish species and GIS maps for the two main commercial fish species Blueskin Seabream and Bigeye Hound Shark, Iago omanensis were documented.     

The marine viromes of four oceanic regions

Viruses are the most common biological entities in the marine environment. There has not been a global survey of these viruses, and consequently, it is not known what types of viruses are in Earth's oceans or how they are distributed. Metagenomic analyses of 184 viral assemblages collected over a decade and representing 68 sites in four major oceanic regions showed that most of the viral sequences were not similar to those in the current databases. There was a distinct “marine-ness” quality to the viral assemblages. Global diversity was very high, presumably several hundred thousand of species, and regional richness varied on a North-South latitudinal gradient. The marine regions had different assemblages of viruses. Cyanophages and a newly discovered clade of single-stranded DNA phages dominated the Sargasso Sea sample, whereas prophage-like sequences were most common in the Arctic. However most viral species were found to be widespread. With a majority of shared species between oceanic regions, most of the differences between viral assemblages seemed to be explained by variation in the occurrence of the most common viral species and not by exclusion of different viral genomes. These results support the idea that viruses are widely dispersed and that local environmental conditions enrich for certain viral types through selective pressure.