Coarse-resolution Ecology of Etiological Agent,Vector, and Reservoirs of Zoonotic Cutaneous Leishmaniasis in Libya

Cutaneous leishmaniasis ranks among the tropical diseases least known and most neglected in Libya. World Health Organization reports recognized associations of Phlebotomus papatasi, Psammomys obesus, and Meriones spp., with transmission of zoonotic cutaneous leishmaniasis (ZCL; caused by Leishmania major) across Libya. Here, we map risk of ZCL infection based on occurrence records of L. major, P. papatasi, and four potential animal reservoirs (Meriones libycus, Meriones shawi, Psammomys obesus, and Gerbillus gerbillus). Ecological niche models identified limited risk areas for ZCL across the northern coast of the country; most species associated with ZCL transmission were confined to this same region, but some had ranges extending to central Libya. All ENM predictions were significant based on partial ROC tests. As a further evaluation of L. major ENM predictions, we compared predictions with 98 additional independent records provided by the Libyan National Centre for Disease Control (NCDC); all of these records fell inside the belt predicted as suitable for ZCL. We tested ecological niche similarity among vector, parasite, and reservoir species and could not reject any null hypotheses of niche similarity. Finally, we tested among possible combinations of vector and reservoir that could predict all recent human ZCL cases reported by NCDC; only three combinations could anticipate the distribution of human cases across the country.     

龟鳖目淡水龟科系统发生关系的研究进展

淡水龟科是龟鳖目中物种数目最多、形态变异最多样的一个类群。其早期的系统学研究主要依据形态学和细胞学的特征,近年来,随着分子数据的不断增多,结合形态学等方法,淡水龟科系统发生学研究取得了诸多进展,但至今尚未有一致的结论。本文主要对近年来有关淡水龟科起源的单系性问题;潮龟属、闭壳龟属和拟水龟属重划分问题;潮龟属、草龟属和小棱背龟属属间关系问题;齿缘龟属、果龟属和东方龟属属间关系问题;齿缘龟属和木纹龟属属内种间关系问题研究进行了文献综述,以期为淡水龟科的系统发生关系和物种保护等研究提供参考。     

Global variation in the piggyBac-like element of pink bollworm,Pectinophora gossypiella

The piggyBac transposable element, originally discovered in the cabbage looper, Trichoplusia ni, has been used widely in genetic engineering of insects including the pink bollworm, Pectinophora gossypiella, a major lepidopteran pest of cotton. Previously, we identified an intact copy of a piggyBac-like element (PLE) in pink bollworm, designated as PgPLE1.1. Here we report global variation in the occurrence and sequence of PgPLE1.1 and its flanking sequences. Low to high frequency of the PgPLE1.1 insertion was observed in populations from USA, Mexico, China, India, and Israel, while there is no PgPLE1.1 insertion in the populations from Australia. Investigation of the five haplotypes of PgPLE1.1, their frequency, and the flanking sequences of PgPLE1.1 revealed significant differences of the populations from Australia and China compared to other global populations, although recent occurrences of extensive gene flows among global populations were evident.     

Comparative morphology of the pyloric armature of adult mosquitoes (Diptera: Culicidae)

The structure of the pyloric armature, hypothesized to aid in blood-meal digestion or parasite resistance, was compared quantitatively among the following 8 species in 5 genera of adult mosquitoes from the southeastern United States: Aedes albopictus, Aedes japonicus, Aedes triseriatus, Anopheles punctipennis, Culex pipiens s.l., Culex restuans, Orthopodomyia signifera, and Toxorhynchites rutilus. Females differed significantly among species in the structure of spines composing the armature, with Aedes spp. forming one general group, Culex spp. another, and An. punctipennis and Or. signifera a third. Relationships of species based on structural characters of the armature were consistent with recent culicid phylogenies. Although pyloric armature has been noted in mosquitoes and other insects, this is the first quantitative investigation of the mosquito pyloric armature.     

A phylogenetic investigation of the Neotropical genus Alphamenes van der Vecht, 1977 (Hymenoptera,Vespidae, Eumeninae)

Advances in potter wasp systematics have been achieved recently, with classificatory changes resulting from analyses based upon large scale molecular datasets. For the Neotropics, recent hypotheses point to the occurrence of an exclusive clade recognized within the tribe Eumenini. In this group, several contributions regarding taxonomy and systematics have been proposed in the last five years, including the genus Alphamenes. This taxon contains seven described species whose distribution is exclusively Neotropical. Females are morphologically homogeneous, and characters related to copulatory organs are useful in male diagnosis. This contribution forms the first phylogenetic approach to include all species of Alphamenes, hence the first to strongly test for group monophyly. Our cladistic results recovered Alphamenes as a monophyletic group supported by male genital features. Relationships among included species also rely upon genitalic characters, highlighting the importance of these attributes for eumenine systematics. Recent phylogenetic investigations applied to the Neotropical fauna of potter wasps represent desirable advancements towards a natural classification for the group.     

Effects of Medicago truncatula Genetic Diversity, Rhizobial Competition, and Strain Effectiveness on the Diversity of a Natural Sinorhizobium Species Community

We investigated the genetic diversity and symbiotic efficiency of 223 Sinorhizobium sp. isolates sampled from a single Mediterranean soil and trapped with four Medicago truncatula lines. DNA molecular polymorphism was estimated by capillary electrophoresis-single-stranded conformation polymorphism and restriction fragment length polymorphism on five loci (IGS_NOD, typA, virB11, avhB11, and the 16S rRNA gene). More than 90% of the rhizobia isolated belonged to the Sinorhizobium medicae species (others belonged to Sinorhizobium meliloti), with different proportions of the two species among the four M. truncatula lines. The S. meliloti population was more diverse than that of S. medicae, and significant genetic differentiation among bacterial populations was detected. Single inoculations performed in tubes with each bacterial genotype and each plant line showed significant bacterium-plant line interactions for nodulation and N₂ fixation levels. Competition experiments within each species highlighted either strong or weak competition among genotypes within S. medicae and S. meliloti, respectively. Interspecies competition experiments showed S. meliloti to be more competitive than S. medicae for nodulation. Although not highly divergent at a nucleotide level, isolates collected from this single soil sample displayed wide polymorphism for both nodulation and N₂ fixation. Each M. truncatula line might influence Sinorhizobium soil population diversity differently via its symbiotic preferences. Our data suggested that the two species did not evolve similarly, with S. meliloti showing polymorphism and variable selective pressures and S. medicae showing traces of a recent demographic expansion. Strain effectiveness might have played a role in the species and genotype proportions, but in conjunction with strain adaptation to environmental factors.     

Genetic Population Structure of Pacific Hake, Merluccius productus, in the Pacific Northwest

This study presents the first protein electrophoretic study of population structure within the Georgia Basin Pacific hake Distinct Population Segment, as defined under the U.S. Endangered Species Act. Forty-one allozyme loci (29 polymorphic) were analyzed in samples from three Pacific hake spawning populations on the west coast of North America: (1) Port Susan, Puget Sound, Washington (three temporal samples); (2) south-central Strait of Georgia, British Columbia, Canada (two temporal samples); and (3) offshore of southern California (two temporal samples) (total n = 664). Mean heterozygosity over all loci was 12–13% for all populations. Within-population temporal samples were not significantly different from one another, but statistically significant differences were detected at 15 of the 29 polymorphic loci (p < 0.05) among the three populations. Differences at eight of these loci were highly significant (p < 0.001): ADA ^*, ALAT ^*, bGALA ^*, GPI-A ^*, sIDHP ^*, LDH-A ^*, MPI ^*, and PEP-B ^*. The two Georgia Basin populations were significantly different at six loci: bGALA ^*, sIDHP ^*, LDH-A ^*, MPI ^*, PGK ^*, and PGM-2 ^* (p < 0.05). Nei's genetic distance (D) was 0.0006 between Port Susan and Strait of Georgia pooled temporal samples, and 0.005 between these populations and offshore Pacific hake. F_ST was 0.02 and 0.0046 among all three populations and among the Georgia Basin populations, respectively. Both F_ST estimates were significantly greater than zero, and the results suggest a high degree of demographic isolation among all three populations.     

Diversity, Geographic Distribution and Conservation of Squirrel Monkeys, Saimiri (Primates, Cebidae), in the Floodplain Forests of Central Amazon

Eleven taxa of primates are found in the floodplains of the western portion of the central Brazilian Amazon, protected in part by the Mamirauá Sustainable Development Reserve. The taxonomy of the squirrel monkeys, the number of taxa, and their geographic distributions are still poorly understood. Here we investigate differentiation among the taxa of this genus in Mamirauá, examining their morphology and geographic distribution. We registered 333 points of occurrence of squirrel monkeys and examined 117 specimens deposited in scientific collections. The results of the morphological analyses were generally in good agreement with field observations. Together they indicate the existence of three taxa: Saimiri vanzolinii, Saimiri sciureus macrodon, and S. s. cassiquiarensis. The restricted range of Saimiri vanzolinii in the southeastern portion of the reserve covers an area of 870 km², and it is among the smallest of the distribution areas for any Neotropical primate species. Saimiri sciureus cassiquiarensis has a disjunct distribution, crossing the Japurá River to the right bank into the reserve in two places, and S. s. macrodon is the squirrel monkey ranging widely in the northwest of Mamirauá. There are three areas of parapatry: one between Saimiri vanzolinii and Saimiri sciureus macrodon and two between S. vanzolinii and S. s. cassiquiarensis. We recommend that anthropogenic changes in the region be monitored, and conservation measures be taken to protect these primates, especially considering the endemism and very restricted range of Saimiri vanzolinii and its consequent vulnerability to extinction.     

Host Adaptation of Chlamydia pecorum towards Low Virulence Evident in Co-Evolution of the ompA,incA, and ORF663 Loci

Chlamydia (C.) pecorum, an obligate intracellular bacterium, may cause severe diseases in ruminants, swine and koalas, although asymptomatic infections are the norm. Recently, we identified genetic polymorphisms in the ompA, incA and ORF663 genes that potentially differentiate between high-virulence C. pecorum isolates from diseased animals and low-virulence isolates from asymptomatic animals. Here, we expand these findings by including additional ruminant, swine, and koala strains. Coding tandem repeats (CTRs) at the incA locus encoded a variable number of repeats of APA or AGA amino acid motifs. Addition of any non-APA/AGA repeat motif, such as APEVPA, APAVPA, APE, or APAPE, associated with low virulence (P<10⁻⁴), as did a high number of amino acids in all incA CTRs (P = 0.0028). In ORF663, high numbers of 15-mer CTRs correlated with low virulence (P = 0.0001). Correction for ompA phylogram position in ORF663 and incA abolished the correlation between genetic changes and virulence, demonstrating co-evolution of ompA, incA, and ORF663 towards low virulence. Pairwise divergence of ompA, incA, and ORF663 among isolates from healthy animals was significantly higher than among strains isolated from diseased animals (P≤10⁻⁵), confirming the longer evolutionary path traversed by low-virulence strains. All three markers combined identified 43 unique strains and 4 pairs of identical strains among all 57 isolates tested, demonstrating the suitability of these markers for epidemiological investigations.     

Population genetic structure of the Staphylococcus intermedius group: insights into agr diversification and the emergence of methicillin-resistant strains

The population genetic structure of the animal pathogen Staphylococcus intermedius is poorly understood. We carried out a multilocus sequence phylogenetic analysis of isolates from broad host and geographic origins to investigate inter- and intraspecies diversity. We found that isolates phenotypically identified as S. intermedius are differentiated into three closely related species, S. intermedius, Staphylococcus pseudintermedius, and Staphylococcus delphini. S. pseudintermedius, not S. intermedius, is the common cause of canine pyoderma and occasionally causes zoonotic infections of humans. Over 60 extant STs were identified among the S. pseudintermedius isolates examined, including several that were distributed on different continents. As the agr quorum-sensing system of staphylococci is thought to have evolved along lines of speciation within the genus, we examined the allelic variation of agrD, which encodes the autoinducing peptide (AIP). Four AIP variants were encoded by S. pseudintermedius isolates, and identical AIP variants were shared among the three species, suggesting that a common quorum-sensing capacity has been conserved in spite of species differentiation in largely distinct ecological niches. A lack of clonal association of agr alleles suggests that assortive recombination may have contributed to the distribution of agr diversity. Finally, we discovered that the recent emergence of methicillin-resistant strains was due to multiple acquisitions of the mecA gene by different S. pseudintermedius clones found on different continents. Taken together, these data have resolved the population genetic structure of the S. intermedius group, resulting in new insights into its ancient and recent evolution.     

Relationships of the dissected elaphoglossoid ferns

The pedately dividedElaphoglossum cardenasii and the two small genera,Peltapteris andMicrostaphyla, are found to have close relatives among the entire-bladed species ofElaphoglossum, supporting the view that all the dissected forms should be considered as species ofElaphoglossum. Necessary nomenclatural changes are made.     

Esterase Allozymes of Soybean Cyst Nematode,Heterodera glycines,from China,Japan, and the United States

Individual females from 19 populations of Heterodera glycines from China, Japan, and the United States were analyzed for esterase allozyme polymorphism. Eight esterase electrophoretic phenotypes were resolved. Four putative loci, est-1, est-2, est-3, and est-4, were identified, having one, one, two, and one allele, respectively. The four loci expressed six genotypes in the four Chinese populations. Loci est-2, est-3, and est-4 were identified in five Japanese populations and expressed five genotypes, whereas only loci est-2 and est-3 were identified in 10 populations from the United States and expressed four genotypes. Putative alleles at each locus were defined as characters for data analysis. Phylogenetic analysis using parsimony (PAUP) was utilized to determine relationships among the 19 populations. More loci and alleles in populations from China and phylogenetic similarities among populations from Japan and the United States are consistent with a founder effect resulting from dissemination of progenitor H. glycines from China to Japan and subsequent introductions of founder populations from Japan to the United States.     

Characterization of a novel alphabaculovirus isolated from the Southern armyworm,Spodoptera eridania (Cramer, 1782) (Lepidoptera: Noctuidae) and the evolution of odv-e66, a bacterium-acquired baculoviral chondroitinase gene

The Southern armyworm Spodoptera eridania (Lepidoptera: Noctuidae) is native to the American tropics and a polyphagous pest of several crops. Here we characterized a novel alphabaculovirus isolated from S. eridania, isolate Spodoptera eridania nucleopolyhedrivurus CNPSo-165 (SperNPV-CNPSo-165). SperNPV-CNPSo-165 occlusion bodies were found to be polyhedral and to contain virions with multiple nucleocapsids. The virus was lethal to S. eridania and S. albula but not to S. frugiperda. The SperNPV-CNPSo-165 genome was 137.373 bp in size with a G + C content of 42.8%. We annotated 151 ORFs with 16 ORFs unique among baculoviruses. Phylogenetic inference indicated that this virus was closely related to the most recent common ancestor of other Spodoptera-isolated viruses.     

Rare species of cyclostomata and fish in the Upper Oka basin and within Kaluga oblast

The species list of fish of the Upper Oka basin is verified. Data on biology of rare species are presented (western brook lamprey Lampetra planeri, sterlet Acipenser ruthenus, bystryanka Alburnoides bipunctatus rossicus, asp Aspius aspius, undermouth Chondrostoma variabile, bitterling Rhodeus sericeus, and fresh-water sculpin Cottus gobio koshewnikowi). Their morphological characters, distribution in the Upper Oka basin relative abundances of these species, and its changes during recent decades are also commented.     

Genetic structure and historical demography of Collichthys lucidus inferred from mtDNA sequence analysis

Fluctuations of global climate changes during the Pleistocene had a huge impact on the marginal seas of the Northwestern Pacific. To examine historical demography and the population genetic structure of Collichthys lucidus, a total of 151 individuals from 7 locations were sequenced at the 5′ end of mitochondrial DNA control region and 380-bp fragments were obtained. The results of AMOVA showed that the genetic variation among the two groups was 78.39 % (P?=?0.78) and among populations within groups was 0.43 % (P?=?0.02). Both mismatch distribution analysis and neutrality tests showed C. lucidus has experienced a recent population expansion. Three distinct clades suggested that C. lucidus might be isolated in the three marginal seas during the Pleistocene periods. No genetic divergence within groups should be explained by insufficient time to attain migration-drift equilibrium. The changes in sea level during the Pleistocene had a major effect on the C. lucidus phylogeographical pattern because it limited its dispersal and at times created isolated populations.     

Assessment of Tumor Heterogeneity,as Evidenced by Gene Expression Profiles,Pathway Activation,and Gene Copy Number,in Patients with Multifocal Invasive Lobular Breast Tumors

BackgroundInvasive lobular carcinoma (ILC) comprises approximately ~10–20% of breast cancers. In general, multifocal/multicentric (MF/MC) breast cancer has been associated with an increased rate of regional lymph node metastases. Tumor heterogeneity between foci represents a largely unstudied source of genomic variation in those rare patients with MF/MC ILC.MethodsWe characterized gene expression and copy number in 2 or more foci from 11 patients with MF/MC ILC (all ER+, HER2-) and adjacent normal tissue. RNA and DNA were extracted from 3x1.5mm cores from all foci. Gene expression (730 genes) and copy number (80 genes) were measured using Nanostring PanCancer and Cancer CNV panels. Linear mixed models were employed to compare expression in tumor versus normal samples from the same patient, and to assess heterogeneity (variability) in expression among multiple ILC within an individual.Results35 and 34 genes were upregulated (FC>2) and down-regulated (FC<0.5) respectively in ILC tumor relative to adjacent normal tissue, q<0.05. 9/34 down-regulated genes (FIGF, RELN, PROM1, SFRP1, MMP7, NTRK2, LAMB3, SPRY2, KIT) had changes larger than CDH1, a hallmark of ILC. Copy number changes in these patients were relatively few but consistent across foci within each patient. Amplification of three genes (CCND1, FADD, ORAOV1) at 11q13.3 was present in 2/11 patients in both foci. We observed significant evidence of within-patient between-foci variability (heterogeneity) in gene expression for 466 genes (p<0.05 with FDR 8%), including CDH1, FIGF, RELN, SFRP1, MMP7, NTRK2, LAMB3, SPRY2 and KIT.ConclusionsThere was substantial variation in gene expression between ILC foci within patients, including known markers of ILC, suggesting an additional level of complexity that should be addressed.     

Species identity and phylogenetic relationship of the pearl oysters in Pinctada Röding, 1798 based on ITS sequence analysis

Analysis of ITS 1 and ITS 2 sequences in the pearl oysters Pinctada albina, Pinctada chemnitzi, Pinctada fucata, Pinctada fucata martensii, Pinctada imbricata, Pinctada margaritifera, Pinctada maxima, Pinctada nigra and Pinctada radiata was carried out. Homogeneity test of substitution patterns suggests that GC contents are highest in P. margaritifera and P. maxima and chromosomal rearrangements occurred in P. chemnitzi. These observations indicate that P. margaritifera and P. maxima are primitive species and P. chemnitzi is a recent species. Phylogenetic analysis shows that the pearl oysters studied constitute three clades with P. margaritifera and P. maxima forming the basal clade, congruent with results revealed by the substitution pattern test. The second clade consists of P. fucata, P. fucata martensii and P. imbricata. Low genetic distances among these taxa indicate that they may be conspecific. The remaining species make up the third clade and low genetic divergence between P. albina and P. nigra suggests that they may represent the same species. The ITS 1 sequence of P. radiata in GenBank is almost identical to that of P. chemnitzi determined in the present study and we suspect that the specimen used for the P. radiata sequence was misidentified.     

Spatial,temporal and interindividual epigenetic variation of functionally important DNA methylation patterns

DNA methylation is an epigenetic modification that plays an important role in gene regulation. It can be influenced by stochastic events, environmental factors and developmental programs. However, little is known about the natural variation of gene-specific methylation patterns. In this study, we performed quantitative methylation analyses of six differentially methylated imprinted genes (H19, MEG3, LIT1, NESP55, PEG3 and SNRPN), one hypermethylated pluripotency gene (OCT4) and one hypomethylated tumor suppressor gene (APC) in chorionic villus, fetal and adult cortex, and adult blood samples. Both average methylation level and range of methylation variation depended on the gene locus, tissue type and/or developmental stage. We found considerable variability of functionally important methylation patterns among unrelated healthy individuals and a trend toward more similar methylation levels in monozygotic twins than in dizygotic twins. Imprinted genes showed relatively little methylation changes associated with aging in individuals who are >25 years. The relative differences in methylation among neighboring CpGs in the generally hypomethylated APC promoter may not only reflect stochastic fluctuations but also depend on the tissue type. Our results are consistent with the view that most methylation variation may arise after fertilization, leading to epigenetic mosaicism.     

Pollen morphology and its taxonomic significance in the tribe Gochnatieae (Compositae, Gochnatioideae)

In the context of recent molecular phylogenies of the basal grades of Compositae, we investigated the utility of pollen morphology within the tribe Gochnatieae. The pollen of 64 species of Anastraphia, Cnicothamnus, Cyclolepis, Gochnatia, Pentaphorus, and Richterago was studied using light microscopy and scanning electron microscopy. In addition, three extra-Gochnatieae genera (Ianthopappus, Leucomeris, and Nouelia) were examined as they were traditionally morphologically related to members of the tribe Gochnatieae. Three of the species of Gochnatieae were examined using transmission electron microscopy. Two pollen types, and two new subtypes, have been recognized on the basis of the pollen shape, size, and exine sculpture. The pollen features of Gochnatia sect. Moquiniastrum and G. cordata are similar and distinctive within the genus and support the recently re-circumscribed section Hedraiophyllum. Within the species with echinate pollen surface, the distinctive spine length of Anastraphia supports its recent resurrection as a genus. The identity of Pentaphorus could not be supported by pollen features as was for other morphological characteristics. The pollen features shared across Cyclolepis, Ianthopappus, Leucomeris, Nouelia and Gochnatia sect. Moquiniastrum, as well as those shared by Richterago and Anastraphia could be a result of parallel evolution.     

Acetate formation in the energy metabolism of parasitic helminths and protists

Formation and excretion of acetate as a metabolic end product of energy metabolism occurs in many protist and helminth parasites, such as the parasitic helminths Fasciola hepatica, Haemonchus contortus and Ascaris suum, and the protist parasites, Giardia lamblia, Entamoeba histolytica, Trichomonas vaginalis as well as Trypanosoma and Leishmania spp. In all of these parasites acetate is a main end product of their energy metabolism, whereas acetate formation does not occur in their mammalian hosts. Acetate production might therefore harbour novel targets for the development of new anti-parasitic drugs. In parasites, acetate is produced from acetyl-CoA by two different reactions, both involving substrate level phosphorylation, that are catalysed by either a cytosolic acetyl-CoA synthetase (ACS) or an organellar acetate:succinate CoA-transferase (ASCT). The ACS reaction is directly coupled to ATP synthesis, whereas the ASCT reaction yields succinyl-CoA for ATP formation via succinyl-CoA synthetase (SCS). Based on recent work on the ASCTs of F. hepatica, T. vaginalis and Trypanosoma brucei we suggest the existence of three subfamilies of enzymes within the CoA-transferase family I. Enzymes of these three subfamilies catalyse the ASCT reaction in eukaryotes via the same mechanism, but the subfamilies share little sequence homology. The CoA-transferases of the three subfamilies are all present inside ATP-producing organelles of parasites, those of subfamily IA in the mitochondria of trypanosomatids, subfamily IB in the mitochondria of parasitic worms and subfamily IC in hydrogenosome-bearing parasites. Together with the recent characterisation among non-parasitic protists of yet a third route of acetate formation involving acetate kinase (ACK) and phosphotransacetylase (PTA) that was previously unknown among eukaryotes, these recent developments provide a good opportunity to have a closer look at eukaryotic acetate formation.