Friday, September 19, 2014

A social media experiment

Boxes waiting to be picked up
The School Malaise Trap Program is up and running again!

Last week boxes filled with Malaise traps and supplies went out to 60 schools across Canada. Starting next week classrooms will collect insects on their school yards and we will be helping them by barcoding some of their finds. 

It is the 4th run of this very successful educational program and this time we were seriously oversubscribed. For the 60 slots we have available over 150 schools applied and our only marketing was a single email during the summer break announcing it to principals and teachers in Canada. For the first time we offered it outside of Ontario and as you can see from the map we have quite a few schools from other provinces.

We've also started an experiment with social media by inviting all participating classrooms to blog about their experiences. The blog on the programs website is also intended to stimulate dialog between the different schools which in some cases are more than 5000 km away from each other.

The main reason to limit the number of participating schools is limited amounts of funding available to us. For the same reason we are not offering it outside of Canada so far although it would be fairly straightforward to do so. I have been overseeing this project for 2 years now and every time I was amazed how much it meant to the kids to be able to participate at such a program. Part of my job is to pass on some of that excitement to people that are looking for new, meaningful ways to invest their money. Fingers crossed for the coming years.

Thursday, September 18, 2014

DNA Barcoding and killing agents

source INBio Costa Rica
[..] sequencing projects require the collection of large numbers of specimens, which need to be killed and preserved in a way that is both DNA-friendly and which will keep voucher specimens in good condition for later study. Factors such as time since collection, correct storage (exposure to free water and heat) and DNA extraction protocol are known to play a role in the success of downstream molecular applications. Limited data are available on the most efficient, DNA-friendly protocol for killing. In this study we evaluate the quality of DNA barcode (cytochrome oxidase I) sequences amplified from DNA extracted from specimens collected using three different killing methods (ethyl acetate, cyanide and freezing). 

This is part of an abstract to a brand-new paper that just appeared in Molecular Ecology Resources. Ever since we started using molecular methods it has been one of the most discussed issues and many researchers started with the question what killing and preservation method should be used to ensure sufficient DNA quality while keeping the potential voucher specimen intact? Chemicals such as ethyl acetate and formaldehyde have been discussed as substances that have the potential to degrade DNA and as such may not be appropriate for the collection of samples for any DNA-based research. Especially formaldehyde represents an issue as killing agent but even more so as preservation liquid. It still is probably the most widely used preservation option we have. It is cheap and provides stable long term storage conditions that keep a specimen intact for future morphological analysis. However, especially over a longer period it will inevitable destroy DNA in an irreversible manner. Colleagues have looked into this issue in a lot of detail simply because most museum fluid collections are using formaldehyde and therefore seem to be lost for any molecular work. 

As for killing methods entomologists are mostly using either ethyl acetate, cyanide or freezing. A molecular biologist would probably always advise to use freezing. No chemical involved would mean no risk for DNA damage and assuming the temperature is low enough it would also help to keep the specimen intact (including coloration). However, in the field very often this is not suitable as you either have to transport the animals alive to the next available freezer or even take a cryogenic shipper with you. Ethanol or other liquids (DMSO-solution, RNAlater) would be an alternative as well and are certainly not DNA-damaging. However, the killing and storage of insect specimens in solutions may not be appropriate for groups where fragile morphological features such as scales on external parts of the body such as the wings may be damaged by wet killing and storage. Furthermore, most insect collections contain pinned specimens and those are in much better shape if they haven't been in any liquid before. 

In this study the colleagues from the University of KwaZulu-Natal in South Africa examined the recoverability of DNA Barcodes from lepidoptera specimens collected using the three common methods described above. Their results are intriguing although currently limited to one insect order. 

All Lepidoptera collected produced DNA barcodes of good quality and our study found no clear difference in nucleotide signal strength, probability of incorrect base calling and phylogenetic utility among the three different treatment groups. Our findings suggest that ethyl acetate, cyanide and freezing can all be used to collect specimens for DNA analysis. 

I am fairly confident that future studies with other arthropod groups will show similar results although I can imagine that issues rather correlate with specimen size or duration of treatment.

Wednesday, September 17, 2014

Blastocystis in dogs and cats

Companion animals (specifically, domestic dogs and cats) are prone to several protozoan gastrointestinal infections, with Giardia duodenalis [syn. G. lamblia, G. intestinalis] and Cryptosporidium parvum both being of significant concern in animals with gastrointestinal disease, and as potential zoonotic infections. Recently, increasing interest has been given to the stramenopile organism Blastocystis spp. as a potential cause of gastrointestinal disease in human beings.

Human infections are found at a rate of 5-10% in most developed countries with elevated rates for individuals that work with animals. In developing countries the rate can be as high as 50%. However, only 50% and 80% of individuals infected with Blastocystis will show any symptoms. Symptoms associated with the infection are diarrhea, nausea, abdominal cramps, bloating, and excessive gas. Most cases of the infection are diagnosed as irritable bowel syndrome, which is actually a symptom-based diagnosis with no known organic cause but characterized by the very same symptoms. 

Because of a growing interest in Blastocystis as a potential enteric pathogen, and the possible role of domestic and in-contact animals as reservoirs for human infection, researchers of the College of Veterinary Medicine at Oregon State University tried to estimate the prevalence of Blastocystis spp. in shelter-resident and client-owned companion animals in the US Pacific Northwest region.

They used the proposed DNA Barcode standard for protists, 18S (or SSU rRNA) to detect the presence of Blastocystis sp. Their findings indicate that shelter-resident animals were carrying a variety of Blastocystis subtype while they couldn't detect the protist in any fecal sample from client-owned animals. In addition no relationship was seen between Blastocystis carriage and the presence of gastrointestinal disease signs in either dogs or cats. These data suggest that, as previously reported for other enteric pathogens, shelter-resident companion animals are a higher risk for carriage of Blastocystis spp. The lack of relationship between Blastocystis carriage and intestinal disease in shelter-resident animals suggests that this organism is unlikely to be a major enteric pathogen in these species.

There is more good news especially for those that want to adopt shelter animals. The majority of identifiable specimens belonged to a subtype with no evidence of carriage in human beings. Therefore, it is unlikely that shelter resident animals in the Pacific Northwest of the USA represent a potential risk for zoonotic infection of animal handlers or owners.

Tuesday, September 16, 2014

Discoveries of the week

Spasskia brevicarinata
The genus Spasskia Belokobylskij, 1989 (Hymenoptera: Braconidae: Helconinae) is reported for the first time from China. Two species, namely Spasskia brevicarinata Yan et Chen sp. n. and Spasskia indica Singh, Belokobylskij et Chauhan, 2005 are described and illustrated. A key to the species of this genus is updated to include the new species.

The new species is rather small - adults are less than one centimeter long. It is similar to a previously described species called Spasskia indica, but the ridges on some of its body segments are different. In fact, the species epithet brevicarinata refers to a short ridge on its first tergite, as "brevi" is Latin for short and "carinata" is Latin for ridge.

no DNA barcode

A new species of Neoplecostomus is described from the rio Doce basin representing the first species of this genus in the basin. The new species is distinguished from its congeners by having enlarged, fleshy folds between dentaries, two or three series of developed papillae anterior to premaxillary teeth and a adipose-fin membrane present, and by lacking enlarged odontodes along snout lateral margins in mature males, a well-developed dorsal-fin spinelet wider than dorsal-fin spine base, lower number of lateral-line figs and developed membrane on the dorsal portion of the first, second and third pelvic-fin branched rays. Additionally, we present a brief discussion of biogeographic scenarios that may explain the distribution of the new species in the rio Doce basin. We suggested that the ancestral lineage of the new species reached the rio Doce from the upper portions of rio Paraná drainages about 3.5 Mya (95% HPD: 1.6–5.5) indicating a colonization route of the N. doceensis ancestral lineage from the south end of Serra do Espinhaço, probably as a result of headwater capture processes between the upper rio Paraná and rio Doce basins.

Neoplecostomus is one genus of armored catfishes which are native to South America. The Loricarids are extremely diverse and for a long while a good number of species only had a number with an 'L' as prefix. There are still many of those out there and a large number of specimens with provisional names. The name doceensis for this species is a Latin noun meaning being located or having connection with the Rio Doce basin. This hydrographic system is located in the southeastern region of Brazil.

The present study reports on three species of terrestrial isopods from western Iran. The genus Mongoloniscus Verhoeff, 1930 is recorded for the first time from Iran, with description of a new species: M. persicus sp. n. Protracheoniscus ehsani sp. n. is described and P. darevskii Borutzky, 1975 is redescribed based on Iranian specimens. The diagnostic characters of these species are figured and their geographical distribution is presented on a map.

Woodlice are terrestrial crustaceans with a rigid, segmented, long exoskeleton. This isopod group comprises over 5,000 known species and now two more have been added to the list. The first species is named after the old name for Iran, Persia. The second species was named after a friend of the author who tragically passed away during a field study.
no DNA barcodes

Three new species of the genus Senecio (Asteraceae, Senecioneae) belonging to Senecio ser. Suffruticosi subser. Caespitosi were discovered in the tributaries of the upper Tambo River, Moquegua Department, South Peru. Descriptions, diagnoses and discussions about their distribution, a table with the morphological similarities with other species of Senecio, a distribution map, conservation status assessments, and a key to the caespitose Peruvian species of Senecio subser. Caespitosi are provided. The new species are Senecio moqueguensis Montesinos, sp. nov. (Critically Endangered) which most closely resembles Senecio pucapampaensis Beltrán, Senecio sykorae Montesinos, sp. nov. (Critically Endangered) which most closely resembles Senecio gamolepis Cabrera, and Senecio tassaensis Montesinos, sp. nov. (Critically Endangered) which most closely resembles Senecio moqueguensis Montesinos.

Senecio is one of the largest genera of flowering plants including ragworts and groundsels. Despite several revisions it still contains some 1500 species. 175 of those occur in Peru and a large number (94) of them are endemic. All three new species are endemics as well and unfortunately all of them have been already categorized as critically endangered.
The name of the first species refers to the region Moquegua, where the species was encountered. The next Senecio is named after Karlè Sýkora, a well-known Dutch vegetation scientist who was the authors mentor in phytosociology. The third species is named after the town of Tassa in the Moquegua Region where the species was found.
no DNA barcodes

The genus Kuzicus was established by Gorochov (1993), and was divided into two subgenera: Kuzicus and Neokuzicus. The type species is Teratura suzukii Matsumura & Shiraki, 1908. He transferred Xiphidiopsis denticulatus Karny, 1926  and Xiphidiopsis cervicercus Tinkham, 1943 to the subgenus Kuzicus (Kuzicus), and described one new species, Kuzicus  (Neokuzicus) uvarovi. Ingrisch & Shishodia (2000) erected another new subgenus Parakuzicus, and described two new  species: Kuzicus (Parakuzicus) cervicus and Kuzicus (Parakuzicus) excavatus, and transferred Xiphidiopsis forficatus Bolívar, 1900 to the subgenus Kuzicus (Parakuzicus). Mao et al. (2009) reviewed the genus Kuzicus from China, and  reported one new species, Kuzicus (Kuzicus) multifidous Mao & Shi, 2009. Up to now, the genus Kuzicus includes 3 subgenera and 13 species all over the world (Bolívar, 1900; Matsumura & Shiraki, 1908; Tinkham, 1943; Gorochov,  1993; Ingrisch & Shishodia, 1998; Ingrisch & Shishodia, 2000; Sänger & Helfert, 2004; Sänger & Helfert, 2006a, 2006b; Ingrisch, 2006; Mao et al., 2009). This paper describes one new species. The type specimen is preserved in the Museum of Hebei University. Morphological images were acquired using Leica DFC 450 digital imaging system. The following conventions were adopted for the specimen measurements: Body—the distance from apex of fastigium of vertex to the posterior margin of tenth abdominal tergite;  tegmen—the distance from the base of tegmen to the apex; hind femur—the distance from base of postfemur to the apex of genicular lobe.

A new grasshopper species with a name derived from the depressed tips of the male cerci.
no DNA barcode

Pseudopaludicola atragula

A new species of Pseudopaludicola is described from human-altered areas originally covered by Semideciduous Forest in northwestern state of São Paulo, southeastern Brazil. Morphologically, the new species differs from four species belonging to the P. pusilla group by the absence of either T-shaped terminal phalanges or toe tips expanded, and from all other congeners except P. canga and P. facureae by possessing an areolate vocal sac, with dark reticulation. The higher duration (300–700 ms) of each single, pulsed note (9–36 nonconcatenated pulses) that compose the call in the new species distinguishes it from all other 14 species of Pseudopaludicola with calls already described (10–290 ms). Absence of harmonics also differ the advertisement call of the new species from the call of its sister species P. facureae, even though these two species presented unexpected low genetic distances. Although we could not identify any single morphological
character distinguishing the new species from P. facureae, a PCA and DFA performed using 12 morphometric variables evidenced significant size differences between these two species.

The species name is derived from the Latin words “atra”, meaning dark, black, and “gula”, meaning throat . The males of this species show a dark throat region which is unusual within the genus Pseudopaludicola.
no DNA barcode (they sequenced 16S and wrongly call it DNA Barcode referring to a paper from 2005 in which COI was deemed not suitable. That should be off the table by now).

Monday, September 15, 2014

Applied evolutionary biology

Two categories of evolutionary challenges result from escalating human impacts on the planet. The first arises from cancers, pathogens and pests that evolve too quickly, and the second from the inability of many valued species to adapt quickly enough. Applied evolutionary biology provides a suite of strategies to address these global challenges that threaten human health, food security, and biodiversity. This review highlights both progress and gaps in genetic, developmental and environmental manipulations across the life sciences that either target the rate and direction of evolution, or reduce the mismatch between organisms and human-altered environments. Increased development and application of these underused tools will be vital in meeting current and future targets for sustainable development.

A team of scientists from Denmark and the USA reviewed current progress in addressing a broad set of challenges in agriculture, medicine and environmental management using evolutionary approaches, approaches that consider species' evolutionary histories and the likelihood of rapid evolutionary adaptation to human activities. Above's quote is from the abstract their paper published in Science. They argue that our ability to solve societal challenges in food security, emerging diseases and biodiversity loss will require evolutionary thinking in order to be effective in the long run. Inattention to this will only lead to greater challenges such as short-lived medicines and agricultural treatments, problems that may ultimately hinder sustainable development.

The study finds an urgent need for better implementation of these approaches, for example in managing the use of antibiotics and pesticides in order to reduce the escalating problem of resistance evolution. Furthermore, current efforts are found insufficient to reduce the accumulating costs from chronic disease and biodiversity loss, two challenges ultimately caused by exposure to food and environments to which people and threatened wildlife are poorly adapted.

Applying evolutionary biology has tremendous potential, because it takes into account how unwanted pests or pathogens may adapt rapidly to our interventions and how highly valued species including humans on the other hand are often very slow to adapt to changing environments through evolution. Not considering such aspects may result in outcomes opposite of those desired, making the pests more resistant to our actions, humans more exposed to diseases and vulnerable species less able to cope with new conditions.

There is no shortage of examples for innovative solutions based on applying knowledge gained from evolutionary biology research. Just one example - farmers in the United States and Australia have used planting of pest-friendly refuges to delay evolution of insect resistance to genetically engineered corn and cotton. These genetically modified crops kill certain pests, but without refuges the pests quickly adapt. Providing refuges of conventional plants has been especially effective for suppressing resistance in the pink bollworm (Pectinophora gossypiella), an invasive pest of cotton. Now, one might have some reservations about genetic engineering but the general concept applies to all situations in which the development of resistance threatens our efforts.

Overall a very interesting read. I couldn't agree more with their final conclusion:

Successful governance of living systems requires understanding evolutionary history as well as contemporary and future evolutionary dynamics. Our current scientific capacity for evolutionarily-informed management does not match the need, but it can be increased through new and more widespread training and collaboration, monitored experimentation, and context-sensitive implementation. Like engineering, which is a multifaceted applied science with common core principles, shared vocabulary and coordinated methods, applied evolutionary biology has the potential to serve society as a predictive and integrative framework for addressing practical concerns in applied biology which share at their core the basic evolutionary principles governing life.

Friday, September 12, 2014

DNA origami

DNA origami are self-assembling biochemical structures that are made up of two types of DNA. To make DNA origami, researchers begin with a biologically derived strand of DNA called the scaffold strand. Then they design customized synthetic strands of DNA, called staple strands. Each staple strand is made up of a specific sequence designed to pair with specific subsequences on the scaffold strand.

Staple strands are introduced into a solution containing the scaffold strand, and the solution is then heated and cooled. During this process, each staple strand attaches to specific sections of the scaffold strand, pulling those sections together and folding the scaffold strand into a specific shape organised by the intrinsic chemical properties of the DNA sequences.

These structures are not just interesting and funny ways for scientists to kill time although the ones shown in the image on the right look indeed funny. Potential applications range from biomedical research to nanoelectronics. Examples include enzyme immobilization, drug carry capsules, and nanotechnological self-assembly of materials. They have also been discussed as active structures for nanorobotic applications such as molecular walkers (artificial molecular motor) on origami and switches for algorithmic computing.

So far DNA origami has been limited to a scaffold strand that is made up some 7,200 bases, creating structures that measure about 70 nm by 90 nm, though the shapes may vary. Researchers from North Carolina State University, Duke University and the University of Copenhagen have now created the world's largest DNA origami. They developed a custom scaffold strand that contained 51 kilobases which resulted in a structure measuring approximately 200 nm by 300 nm.

They also implemented a method to decrease the cost of origami production by improving the chip synthesis platform. The researchers did this by using what is essentially a converted inkjet printer to synthesize DNA directly onto a plastic chip.

Pretty cool stuff.

Thursday, September 11, 2014

What crab is it?

Originally from Asia, the brush-clawed shore crab appeared in Europe in 1993, likely transported through hull fouling or ballast water. The first specimens were found on a ship’s hull of a car-carrier in the harbor of Bremerhaven, Germany. However, no established reproductive population could be found at that time. A year later they started a real invasion at the Atlantic coast near La Rochelle quickly expanding their range north and south along French and Spanish Atlantic coasts. By the early 2000's the crab was encountered in the North Sea, e.g. in the intertidal alien Crassostrea-reefs in the Wadden Sea. Pacific oysters (Crassostrea gigas) have been invading the central Wadden Sea since 1998, predominantly settling on intertidal blue mussel (Mytilus edulis) beds which are increasingly transformed into Crassostrea-reefs. This habitat change is already considered to be a threat for waterbirds losing important feeding sites in the intertidal of the Wadden Sea and now it seems that this new habitat provides an ideal home for another invader.

Until 2005, researchers assumed that they were looking at one particular species, the brush-clawed shore crab Hemigrapsus penicillatus. Then two researchers from Japan described a new sibling species as Hemigrapsus takanoi. That left especially European scientists with a question as both species occur sympatrically in Japan and may thus also coexist in European waters because of their similar ecology or the invader is only one species, but which one?

The distinction of both species using morphological traits is extremely difficult and unreliable. That's were a new study from Germany comes in:

To clarify the identity of the alien species, two mitochondrial (partial COI, partial 16S rDNA) and two nuclear genes (partial sodium-potassium ATPase α-subunit, complete 18S rDNA) of several German and Japanese specimens were analysed. In addition to molecular analyses, key morphological characteristics were assessed. As such this is the first integrative approach providing a specimen-specific analysis and a comparative description of both native and invasive specimens.

The colleagues identified their samples from the Central Wadden Sea as Hemigrapsus takanoi. As it turns out most of the specimens from Japan and a set of GenBank sequences of brush-clawed crabs from Japan, Korea and China which were traditionally classified as Hemigrapsus penicillatus in Asia turned out to be Hemigrapsus takanoi. I leave the conclusion of this study to the authors:

The study underlines the difficulty in distinguishing H. takanoi from H. penicillatus on the basis of morphological characteristics alone. We therefore recommend additional molecular identification of the alien species along the coasts of the Northeast Atlantic because several independent introductions may have resulted in regionally displaced invasions of H. takanoi and/or H. penicillatus. Besides natural dispersal, range expansion of the crabs via Pacific oyster transportations between aquaculture facilities is assumed to have facilitated the spread of the species in Europe. Enhanced alertness in identifying the invader is thus required in regions where intensive aquaculture or mussel transfer is practiced. Special attention should also be paid in areas where port operations are expected to increase in the future.