Finding a common motif of RNA sequences using genetic programming: the GeRNAMo system

We focus on finding a consensus motif of a set of homologous or functionally related RNA molecules. Recent approaches to this problem have been limited to simple motifs, require sequence alignment, and make prior assumptions concerning the data set. We use genetic programming to predict RNA consensus motifs based solely on the data set. Our system -- dubbed GeRNAMo (Genetic programming of RNA Motifs) -- predicts the most common motifs without sequence alignment and is capable of dealing with any motif size. Our program only requires the maximum number of stems in the motif, and if prior knowledge is available the user can specify other attributes of the motif (e.g., the range of the motif's minimum and maximum sizes), thereby increasing both sensitivity and speed. We describe several experiments using either ferritin iron response element (IRE); signal recognition particle (SRP); or microRNA sequences, showing that the most common motif is found repeatedly, and that our system offers substantial advantages over previous methods.     

Chemical sensing of DNT by engineered olfactory yeast strain

With the increasing threat of environmental toxicants including biological and chemical warfare agents, fabricating innovative biomimetic systems to detect these harmful agents is critically important. With the broad objective of developing such a biosensor, here we report the construction of a Saccharomyces cerevisiae strain containing the primary components of the mammalian olfactory signaling pathway. In this engineered yeast strain, WIF-1alpha, olfactory receptor signaling is coupled to green fluorescent protein expression. Using this 'olfactory yeast', we screened for olfactory receptors that could report the presence of the odorant 2,4-dinitrotoluene, an explosive residue mimic. With this approach, we have identified the novel rat olfactory receptor Olfr226, which is closely related to the mouse olfactory receptors Olfr2 and MOR226-1, as a 2,4-dinitrotoluene-responsive receptor.     

Nematodes found in Nile crocodiles in the Kruger National Park,South Africa,with redescriptions of Multicaecum agile (Wedl, 1861) (Heterocheilidae) and Camallanus kaapstaadi Southwell & Kirshner, 1937 (Camallanidae)

Sixteen Nile crocodiles were collected in the Kruger National Park, South Africa and vicinity during 2010 and 2011. A total of 11 nematode species representing six families were recovered. Heterocheilids were the dominant group, comprising five species, with Dujardinascaris madagascariensis (Chabaud & Caballero, 1966) being the most prevalent (75%), followed by Ingwenascaris sprenti Junker & Mutafchiev, 2017 (68.8%), which was also the second most numerous nematode. While less prevalent (31.3%), Typhlophoros kwenae Junker & Mutafchiev, 2017 was the most abundant species. Micropleura huchzermeyeri Junker & Mutafchiev, 2017 (Micropleuridae) was collected from five crocodiles and Crocodylocapillaria sp. (Capillariidae) occurred in a single host. Three nematodes, Camallanus kaapstaadi Southwell & Kirshner, 1937, Spirocamallanus sp. (both Camallanidae) and Ascarophis sp. (Cystidicolidae), are considered accidental infections, likely ingested with the hosts’ prey. Our findings of D. dujardini (Travassos, 1920), D. madagascariensis and Multicaecum agile (Wedl, 1861) in South Africa constitute new geographical records. Crocodylocapillaria sp. represents a new host and geographical record, while T. kwenae, I. sprenti and M. huchzermeyeri have been described as new species during the course of this survey. Multicaecum agile is here redescribed based on light and scanning electron microscopy. Previously undescribed morphological characters of C. kaapstaadi, typically a parasite of Xenopus spp. (Amphibia: Pipidae), but here found in two Nile crocodiles, are also presented.

     

Characterisation of Haemonchus contortus-derived cell populations propagated in vitro in a tissue culture environment and their potential to induce protective immunity in sheep

Cell populations derived from viable Haemonchus contortus L(3) larvae were propagated in vitro in a tissue culture environment for a prolonged period (>48 months). Microscopic evaluation of H. contortus-derived cell populations revealed gross morphological characteristics highly analogous to those described for cell types originating from species of plant nematodes propagated in vitro in a tissue culture environment for a briefer period of time (<6 months). The characterisation of extracts harvested from tissue culture populations of H. contortus-derived cells by SDS-PAGE analysis detected molecular fractions of approximately 29, 45, 55, and 200-kDa that closely correlated with reports for preparations obtained from intact/viable H. contortus larvae. Complementary investigations detected the dual biochemical expression of phosphohydrolase and aminopeptidase-M activities based on the hydrolysis of the synthetic enzyme-specific substrates, para-nitrophenylphosphate and leucine-para-nitroanaline, respectively. The identification of phosphohydrolase and aminopeptidase-M-like biochemical activity in fractions harvested from H. contortus-derived cell populations and propagated in vitro in tissue culture served as evidence validating their parasitic-origin. Further validation of H. contortus-derived cell populations propagated in tissue culture entailed the formulation of Triton X-100 extracts containing potential immunoprotective antigens with SEAM adjuvant and its administration by intramuscular injection (100 microg total protein) to healthy sheep (n=8) on day 0 (left rear-limb) and day +14 (right rear-limb). Animals on day 28 subsequently received a single oral challenge of 10,000 infective L(3)-stage H. contortus larvae. Applying ELISA methodologies, increases in antigen-specific IgM and IgG were detected in ovine serum samples. Interpretation of experimental findings revealed that sheep with the greatest antigen-specific humoral immune responses (IgG titre 1/3125) also demonstrated a degree of reduced abomasal H. contortuslarvae burdens (60% reduction). Polyclonal antibody from immunoprotected sheep was subsequently found to recognise both the: (i), digestive tract; and (ii), antigen extracts associated with intact/viable H. contortus larvae. These experimental findings reveal the potential feasibility of propagating parasite-derived cell populations in an in vitro tissue culture environment in a manner that retains their ability to express immunoprotective antigenic fractions.     

Ectoparasites of the swift fox in northwestern Texas

Ectoparasites were collected from chemically immobilized swift foxes (Vulpes velox) in the Texas Panhandle (USA). Three species of fleas (Pulex irritans, Dactylopsylla percernis, and Euhoplopsyllus affinis) and one species of tick (Ixodes sculptus) were found. Pulex irritans was the only abundant ectoparasite; it occurred on all 23 foxes brushed in 1999-2000 and all but one of 34 hosts examined in 2000-01. Otherwise, this swift fox population had a depauperate ectoparasite fauna; the remainder of the ectoparasites only occurred on a few (< or =5%) of the hosts. Because of previous taxonomic confusion between P. irritans and the closely related P. simulans, the zoogeographic distribution of these two species in many areas of western North America needs to be verified. Apparently, only the human flea P. irritans occurs on wild canids in the Texas Panhandle. However, there are previous records of P. simulans on other carnivores in western and central Texas. Some of these specimens were reexamined, and their identifications were reconfirmed. Also, the recent literature on the controversial taxonomic status of these two flea species is reviewed. The male terminal aedeagal sexual apparatus is the only means currently available to separate P. irritans and P. simulans.