Poly(dG)-poly(dC) DNA appears shorter than poly(dA)-poly(dT) and possibly adopts an A-related conformation on a mica surface under ambient conditions

Three types of DNA: approximately 2700 bp polydeoxyguanylic olydeoxycytidylic acid [poly(dG)-poly(dC)], approximately 2700 bp polydeoxyadenylic polydeoxythymidylic acid [poly(dA)-poly(dT)] and 2686 bp linear plasmid pUC19 were deposited on a mica surface and imaged by atomic force microscopy. Contour length measurements show that the average length of poly(dG)-poly(dC) is approximately 30% shorter than that of poly(dA)-poly(dT) and the plasmid. This led us to suggest that individual poly(dG)-poly(dC) molecules are immobilized on mica under ambient conditions in a form which is likely related to the A-form of DNA in contrast to poly(dA)-poly(dT) and random sequence DNA which are immobilized in a form that is related to the DNA B-form.     

CD1d degradation in Chlamydia trachomatis-infected epithelial cells is the result of both cellular and chlamydial proteasomal activity

Chlamydia trachomatis is an obligate intracellular pathogen that can persist in the urogenital tract. Mechanisms by which C. trachomatis evades clearance by host innate immune responses are poorly described. CD1d is MHC-like, is expressed by epithelial cells, and can signal innate immune responses by NK and NKT cells. Here we demonstrate that C. trachomatis infection down-regulates surface-expressed CD1d in human penile urethral epithelial cells through proteasomal degradation. A chlamydial proteasome-like activity factor (CPAF) interacts with the CD1d heavy chain, and CPAF-associated CD1d heavy chain is then ubiquitinated and directed along two distinct proteolytic pathways. The degradation of immature glycosylated CD1d was blocked by the proteasome inhibitor lactacystin but not by MG132, indicating that degradation was not via the conventional proteasome. In contrast, the degradation of non-glycosylated CD1d was blocked by lactacystin and MG132, consistent with conventional cellular cytosolic degradation of N-linked glycoproteins. Immunofluorescent microscopy confirmed the interruption of CD1d trafficking to the cell surface, and the dislocation of CD1d heavy chains into both the cellular cytosol and the chlamydial inclusion along with cytosolic CPAF. C. trachomatis targeted CD1d toward two distinct proteolytic pathways. Decreased CD1d surface expression may help C. trachomatis evade detection by innate immune cells and may promote C. trachomatis persistence.     

Deletion of complement factor H-related genes CFHR1 and CFHR3 is associated with atypical hemolytic uremic syndrome

Atypical hemolytic uremic syndrome (aHUS) is associated with defective complement regulation. Disease-associated mutations have been described in the genes encoding the complement regulators complement factor H, membrane cofactor protein, factor B, and factor I. In this study, we show in two independent cohorts of aHUS patients that deletion of two closely related genes, complement factor H-related 1 (CFHR1) and complement factor H-related 3 (CFHR3), increases the risk of aHUS. Amplification analysis and sequencing of genomic DNA of three affected individuals revealed a chromosomal deletion of approximately 84 kb in the RCA gene cluster, resulting in loss of the genes coding for CFHR1 and CFHR3, but leaving the genomic structure of factor H intact. The CFHR1 and CFHR3 genes are flanked by long homologous repeats with long interspersed nuclear elements (retrotransposons) and we suggest that nonallelic homologous recombination between these repeats results in the loss of the two genes. Impaired protection of erythrocytes from complement activation is observed in the serum of aHUS patients deficient in CFHR1 and CFHR3, thus suggesting a regulatory role for CFHR1 and CFHR3 in complement activation. The identification of CFHR1/CFHR3 deficiency in aHUS patients may lead to the design of new diagnostic approaches, such as enhanced testing for these genes.     

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.

     

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.