Conservation of a 29-base-pair sequence within maxicircle ARS fragments from six species of trypanosomes

The maxicircles from Trypanosoma brucei, Herpetomonas samuelpessoai, Leptomonas seymouri, and Phytomonas davidi were examined for the presence of a 29-bp sequence termed CF29 that has been found in the ars 189 sequence from the Crithidia fasciculata maxicircle and in Lt-ars 189 from the maxicircle of Leishmania tarentolae. The CF29 sequence also contains a yeast consensus ARS of(T/A)TTTATPuTTT(T/A). All of the maxicircles examined contained specific fragments that hybridized to the CF29 probe. The non-replicating yeast plasmid vector YIp5 was used to clone these CF29-containing maxicircle fragments. High-frequency transformation was observed when these chimeric plasmids were used to transform Saccharomyces cerevisiae. Autonomous replication of these transforming plasmids was verified by Southern analysis of yeast-cell extracts using pBR322 as a hybridization probe. Therefore it appears that the CF29 sequence is widely conserved in kinetoplastid protozoa and is associated with ARS sequences in the maxicircles. Hybridization of the CF29 probe to a population of P. davidi minicircles was also observed. However, the YIp5 chimeric plasmid containing this CF29-hybridizing minicircle fragment failed to transform yeast.     

Using urine metabolomics to understand the pathogenesis of infant respiratory syncytial virus (RSV) infection and its role in childhood wheezing

Background

Respiratory syncytial virus (RSV) infection in infants causes significant morbidity and is the strongest risk factor associated with asthma. Metabolites, which reflect the interactions between host cell and virus, provide an opportunity to identify the pathways that underlie severe infections and asthma development.

Objective

To study metabolic profile differences between infants with RSV infection, and human rhinovirus (HRV) infection, and healthy infants. To compare infant metabolic differences between children who do and do not wheeze.

Methods

In a term birth cohort, urine was collected while healthy and during acute viral respiratory infection with RSV and HRV. We used ¹H-NMR to identify urinary metabolites. Multivariate and univariate statistics were used to discriminate metabolic profiles of infants with either RSV ARI, or HRV ARI, and healthy infants. Multivariable logistic regression was used to assess the association of urine metabolites with 1st-, 2nd-, and 3rd-year recurrent wheezing.

Results

Several metabolites in nicotinate and nicotinamide metabolism pathways were down-regulated in infants with RSV infection compared to healthy controls. There were no significant differences in metabolite profiles between infants with RSV infection and infants with HRV Infection. Alanine was strongly associated with reduced risk of 1st-year wheezing (OR 0.18[0.0, 0.46]) and 2nd-year wheezing (OR 0.31[0.13, 0.73]), while 2-hydroxyisobutyric acid was associated with increased 3rd-year wheezing (OR 5.02[1.49, 16.93]) only among the RSV infected subset.

Conclusion

The metabolites associated with infant RSV infection and recurrent-wheezing are indicative of viral takeover of the cellular machinery and resources to enhance virulence, replication, and subversion of the host immune-response, highlighting metabolic pathways important in the pathogenesis of RSV infection and wheeze development.

     

Metabolomic prediction of endometrial cancer

Introduction

Endometrial cancer (EC) is associated with metabolic disturbances including obesity, diabetes and metabolic syndrome. Identifying metabolite biomarkers for EC detection has a crucial role in reducing morbidity and mortality.

Objective

To determine whether metabolomic based biomarkers can detect EC overall and early-stage EC.

Methods

We performed NMR and mass spectrometry based metabolomic analyses of serum in EC cases versus controls. A total of 46 early-stage (FIGO stages I–II) and 10 late-stage (FIGO stages III–IV) EC cases constituted the study group. A total of 60 unaffected control samples were used. Patients and controls were divided randomly into a discovery group (n?=?69) and an independent validation group (n?=?47). Predictive algorithms based on biomarkers and demographic characteristics were generated using logistic regression analysis.

Results

A total of 181 metabolites were evaluated. Extensive changes in metabolite levels were noted in the EC versus the control group. The combination of C14:2, phosphatidylcholine with acyl-alkyl residue sum C38:1 (PCae C38:1) and 3-hydroxybutyric acid had an area under the receiver operating characteristics curve (AUC) (95% CI)?=?0.826 (0.706–0.946) and a sensitivity?=?82.6%, and specificity?=?70.8% for EC overall. For early EC prediction: BMI, C14:2 and PC ae C40:1 had an AUC (95% CI)?=?0.819 (0.689–0.95) and a sensitivity?=?72.2% and specificity?=?79.2% in the validation group.

Conclusions

EC is characterized by significant perturbations in important cellular metabolites. Metabolites accurately detected early-stage EC cases and EC overall which could lead to the development of non-invasive biomarkers for earlier detection of EC and for monitoring disease recurrence.

     

Re-evaluating conservation priorities of New World tarantulas (Araneae: Theraphosidae) in a molecular framework indicates non-monophyly of the genera,Aphonopelma and Brachypelma

We present a mtDNA gene tree of tarantula spiders (Araneae: Mygalomorphae: Theraphosidae) based on the mitochondrial 16S-tRNA (leu)-ND1 gene region as a promising initial molecular hypothesis to clarify the taxonomy of the largest subfamily, Theraphosinae. Many species of this New World subfamily are traded widely as exotic pets, yet few scientific studies on them exist, and the robustness of many supposed taxonomic groupings is debatable. Yet the validity of taxon names and knowledge of their distinctiveness is vital for trade regulation, most notably for the Neotropical genus Brachypelma Simon 1891, which is listed under CITES (Appendix II, see online supplemental material, which is available from the article's Taylor & Francis Online page at https://doi.org/10.1080/14772000.2017.1346719). The use of molecular markers for tarantula taxonomy has been limited until recently, with most previous studies relying on morphological methods. Our findings, from newly collected molecular data, have several nomenclatural implications, suggesting a need for a rigorous overhaul of Theraphosinae classification at multiple hierarchical levels. Here, we take steps toward a revised classification, favouring division of Theraphosinae into three tribes: the Theraphosini trib. nov., the Hapalopini trib. nov., and the Grammostolini trib. nov. We also make conservation recommendations for two non-monophyletic genera. Firstly, we recover Aphonopelma Pocock 1901 as polyphyletic, finding that the large radiation into the USA and Mexico is taxonomically distinct from at least three other lineages distributed throughout Central America, one of which includes the type species of the genus. Secondly, and importantly for conservation, we find diphyly in the CITES listed genus Brachypelma Simon 1891, where our data strongly favour a division into two distinct smaller genera. We consider only the lineage with endemics in the Pacific coastal zone of Mexico to be of conservation concern. Finally, we also make suggestions on the future direction of revisionary research for the Theraphosidae as a whole.

http://zoobank.org/urn:lsid:zoobank.org:pub:B37F7795-3F92-4334-A0C7-65C8026EE1FB     

Development of an X-specific marker and identification of YY individuals in spinach

Spinach is a popular vegetable native to central and western Asia. It is dioecious with a pair of nascent sex chromosomes. The difficulties of working with the non-recombining sex determination region of XY individuals have hindered the progress toward sequencing sex chromosomes of most dioecious species. Here we present important advances toward characterizing the non-recombining sex chromosomes in spinach. Of nearly 400 spinach accessions screened, we identified a single accession of spinach in which androdioecious XY individuals segregate YY spinach. The male and female genomes of the spinach cultivar Shami and USDA accession PI 664497 were sequenced at 12–17?× coverage. X-specific sequences were identified by comparing the depth of coverage differences between male and female alignments to a female draft genome. YY individuals were used as a negative control to validate X-specific markers found by depth of coverage analysis. Of 19 possible X chromosome sequences found by depth of coverage analysis, one was verified to be X-specific by a PCR-based marker, SpoX, which amplified genomic DNA from XX and XY, but not YY templates. Androdioecious XY individuals of accession PI 217425 (Cornell #9) were used to develop inbred lines, and at S7 generation, all XY individuals were androdioecious and all YY individuals were pure male. The sex reversal of the XY mutant to hermaphrodite is strong evidence that the sex chromosomes in spinach have a two-gene sex determination system. These results are crucial towards sequencing the X and Y chromosomes to advance sex chromosome research in spinach.     

A new assemblage of freshwater sharks (Chondrichthyes: Elasmobranchii) from the Upper Triassic of India

This study reports the first occurrence of a varied xenacanth assemblage from the Upper Triassic Tiki Formation of India, based on multiple well-preserved isolated teeth. Based on distinct tooth morphology, two species of the genus Mooreodontus are described: M. indicus and a new species, M. jaini. The new species is diagnosed based on a tricuspid crown containing two stout, slightly diverging lateral cusps pointing in the same direction, a high median cusp, crown-base angle almost at 90°, large, rounded, apical button with several foramina and multiple, 8–9 coarse vertical cristae on all the cusps. Dental anomaly in the form of a partial quadri-cuspidate xenacanthid tooth is present in the collection. Another group of xenacanthid teeth have bicuspid crowns with two upright, asymmetric cusps, where the mesial cusp is thicker than the distal one, and consistently lack a median cusp. Such distinct bicuspid tooth morphology is usually present in Palaeozoic forms and is reported for the first time from the Late Triassic. It is considered to belong to a new taxon, Tikiodontus asymmetricus nov. gen., nov. sp., of indeterminate family. Distinctive tooth histology also differentiates the two Indian genera Mooreodontus and Tikiodontus nov. gen. from other xenacanthid taxa. In addition, the Tiki assemblage has yielded multiple chondrichthyan dermal denticles, which may be subdivided into two morphotypes based on their robustness and presence/absence of linear ridges on the fused cusps. India holds a unique position in terms of its Late Triassic freshwater shark fauna, as it exhibits distinct Laurasian affinities. These freshwater sharks had restricted occurrences in other parts of the Gondwanan landmass.     

A novel receptor‐like kinase involved in fungal pathogen defence in Arabidopsis thaliana

Plants are under constant attack from a variety of disease‐causing organisms. Lacking an adaptive immune system, plants repel pathogen attack via an array of pathogen recognition machinery. Receptor‐like kinases (RLKs) are involved in the recognition of pathogen‐associated molecular patterns (PAMPs) and activate resistance pathways against broad classes of pathogens. We have identified powdery mildew‐resistant kinase 1, an Arabidopsis gene encoding an RLK that is highly induced by chitin at early time points and localizes to the plasma membrane. Knockout mutants in pmrk1 are more susceptible to both Golovinomyces cichoracearum and Plectosphaerella cucumerina. Our data show that PMRK1 is essential in early stages of defence against fungi and provide evidence that PMRK1 may be unique to chitin‐induced signalling pathways. The results of this study indicate that PMRK1 is a critical component of plant innate immunity against fungal pathogens.     

Length–weight relationships for Eutropiichthys murius (Hamilton, 1822), Coilia reynaldi Valenciennes, 1848 and Johnius gangeticus Talwar, 1991 from lower stretch of the River Ganga,India

Length‐weight relationships (LWRs) for three fish species from the River Ganga (India) is presented. Sampling was conducted from the lower stretch of the River Ganga (Patna: 25°36′51.66″N & 85°12′7.02″E to Freserganj: 21°35′40.58″N & 88°15′28.92″E) during April, June and September and December of 2017. Specimens were caught using gill nets (18 nos.; mesh 18–32 mm), and bag nets (3 nos.; mesh 14–22 mm). The values a and b from LWRs ‐were found to be 0.007 and 2.977 for Eutropiichthys murius; 0.003 and 3.001 for Coilia reynaldi; 0.009 and 3.010 for Johnius gangeticus.