Comparative genomics reveals Cyclospora cayetanensis possesses coccidia-like metabolism and invasion components but unique surface antigens

Background

Cyclospora cayetanensis is an apicomplexan that causes diarrhea in humans. The investigation of foodborne outbreaks of cyclosporiasis has been hampered by a lack of genetic data and poor understanding of pathogen biology. In this study we sequenced the genome of C. cayetanensis and inferred its metabolism and invasion components based on comparative genomic analysis.

Results

The genome organization, metabolic capabilities and potential invasion mechanism of C. cayetanensis are very similar to those of Eimeria tenella. Propanoyl-CoA degradation, GPI anchor biosynthesis, and N-glycosylation are some apparent metabolic differences between C. cayetanensis and E. tenella. Unlike Eimeria spp., there are no active LTR-retrotransposons identified in C. cayetanensis. The similar repertoire of host cell invasion-related proteins possessed by all coccidia suggests that C. cayetanensis has an invasion process similar to the one in T. gondii and E. tenella. However, the significant reduction in the number of identifiable rhoptry protein kinases, phosphatases and serine protease inhibitors indicates that monoxenous coccidia, especially C. cayetanensis, have limited capabilities or use a different system to regulate host cell nuclear activities. C. cayetanensis does not possess any cluster of genes encoding the TA4-type SAG surface antigens seen in E. tenella, and may use a different family of surface antigens in initial host cell interactions.

Conclusions

Our findings indicate that C. cayetanensis possesses coccidia-like metabolism and invasion components but unique surface antigens. Amino acid metabolism and post-translation modifications of proteins are some major differences between C. cayetanensis and other apicomplexans. The whole genome sequence data of C. cayetanensis improve our understanding of the biology and evolution of this major foodborne pathogen and facilitate the development of intervention measures and advanced diagnostic tools.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2632-3) contains supplementary material, which is available to authorized users.

Comparative studies on radioluminescent and thermoluminescent spectra of LiF:Mg,Cu,P and LiF:Mg,Cu,Si

The influence of various annealing treatments on radioluminescent (RL) and thermoluminescent (TL) spectra of LiF:Mg,Cu,Si and LiF:Mg,Cu,P was investigated. The TL and RL emission bands for LiF:Mg,Cu,P are not the same; however, the emission band peaking at ∼383 nm is predominant in the TL and RL emission for LiF:Mg,Cu,Si. With the increase in annealing temperatures in the range of 240-300°C, for LiF:Mg,Cu,P, the intensity of TL decreases much more rapidly than that of RL. For LiF:Mg,Cu,Si, the area ratios of the two bands of RL and TL remain constant within experimental errors. It suggests that there is a significant decrease in the concentration of recombination centres in LiF:Mg,Cu,P after the annealing, in addition to the decrease in trapping centres, the recombination centres for main TL emission and RL emission in LiF:Mg,Cu,Si are the same, and the recombination centres for TL emission and RL emission in LiF:Mg,Cu,P are not the same. P is a more effective dopant than Si.

Degradation of Akt using protein-catalyzed capture agents

Abnormal signaling of the protein kinase Akt has been shown to contribute to human diseases such as diabetes and cancer, but Akt has proven to be a challenging target for drugging. Using iterative in situ click chemistry, we recently developed multiple protein-catalyzed capture (PCC) agents that allosterically modulate Akt enzymatic activity in a protein-based assay. Here, we utilize similar PCCs to exploit endogenous protein degradation pathways. We use the modularity of the anti-Akt PCCs to prepare proteolysis targeting chimeric molecules that are shown to promote the rapid degradation of Akt in live cancer cells. These novel proteolysis targeting chimeric molecules demonstrate that the epitope targeting selectivity of PCCs can be coupled with non-traditional drugging moieties to inhibit challenging targets.

From anxious youth to depressed adolescents: Prospective prediction of 2-year depression symptoms via attentional bias measures

Anxious youth are at heightened risk for subsequent development of depression; however, little is known regarding which anxious youth are at the highest prospective risk. Biased attentional patterns (e.g., vigilance and avoidance of negative cues) are implicated as key mechanisms in both anxiety and depression. Aberrant attentional patterns may disrupt opportunities to effectively engage with, and learn from, threatening aspects of the environment during development and/or treatment, compounding risk over time. Sixty-seven anxious youth (ages 9-14; 36 female) completed a dot-probe task to assess baseline attentional patterns provoked by fearful-neutral face pairs. The time course of attentional patterns both during and after threat was assessed via eye-tracking and pupilometry. Self-reported depressive and anxiety symptoms were assessed 2 years after the conclusion of a larger psychotherapy treatment trial. Eye-tracking patterns indicating threat avoidance predicted greater 2-year depression scores, over and above baseline and posttreatment symptoms. Sustained, postthreat pupillary avoidance (reflecting preferential neural engagement with the neutral relative to the previously threatening location) predicted additional variance in depression scores, suggesting sustained avoidance in the wake of threat further exacerbated risk. Identical eye-tracking and pupil indices were not predictive of anxiety at 2 years. These biobehavioral markers imply that avoidant attentional processing in the context of anxiety may be a gateway to depression across a key maturational window. Excessive avoidance of threat could interfere with acquisition of adaptive emotion regulation skills during development, culminating in the broad behavioral deactivation that typifies depression. Prevention efforts explicitly targeting avoidant attentional patterns may be warranted.

Genetic similarities between Cyclospora cayetanensis and cecum-infecting avian Eimeria spp. in apicoplast and mitochondrial genomes

Background

Cyclospora cayetanensis is an important cause for diarrhea in children in developing countries and foodborne outbreaks of cyclosporiasis in industrialized nations. To improve understanding of the basic biology of Cyclospora spp. and development of molecular diagnostic tools and therapeutics, we sequenced the complete apicoplast and mitochondrial genomes of C. cayetanensis.

Methods

The genome of one Chinese C. cayetanensis isolate was sequenced using Roche 454 and Illumina technologies. The assembled genomes of the apicoplast and mitochondrion were retrieved, annotated, and compared with reference genomes for other apicomplexans to infer genome organizations and phylogenetic relationships. Sequence variations in the mitochondrial genome were identified by comparison of two C. cayetanensis nucleotide sequences from this study and a recent publication.

Results

The apicoplast and mitochondrial genomes of C. cayetanensis are 34,155 and 6,229 bp in size and code for 65 and 5 genes, respectively. Comparative genomic analysis showed high similarities between C. cayetanensis and Eimeria tenella in both genomes; they have 85.6 % and 90.4 % nucleotide sequence similarities, respectively, and complete synteny in gene organization. Phylogenetic analysis of the genomic sequences confirmed the genetic similarities between cecum-infecting avian Eimeria spp. and C. cayetanensis. Like in other coccidia, both genomes of C. cayetanensis are transcribed bi-directionally. The apicoplast genome is circular, codes for the complete machinery for protein biosynthesis, and contains two inverted repeats that differ slightly in LSU rRNA gene sequences. In contrast, the mitochondrial genome has a linear concatemer or circular mapping topology. Eight single-nucleotide and one 7-bp multiple-nucleotide variants were detected between the mitochondrial genomes of C. cayetanensis from this and recent studies.

Conclusions

The apicoplast and mitochondrial genomes of C. cayetanensis are highly similar to those of cecum-infecting avian Eimeria spp. in both genome organization and sequences. The availability of sequence data beyond rRNA and heat shock protein genes could facilitate studies of C. cayetanensis biology and development of genotyping tools for investigations of cyclosporiasis outbreaks.

The effects of substance p on tendinopathy are dose-dependent: an in vitro and in vivo model study

OBJECTIVES

Substance P (SP) is known to be involved in neuropathic pain, chronic inflammation, and tendinopathy. The present study evaluated the effects of different doses of SP on tendon-derived stem cells (TDSCs) in vitro and tendons in vivo.

METHODS

For the in vitro study, TDSCs cultured in growth medium with different concentrations of SP (negative control, 0.1 nM, and 1.0 nM). The effects of SP on TDSCs were examined with respect to their ability to proliferate and differentiate. For the in vivo study, we injected different doses of SP (saline control, 0.5 nmol, and 5.0 nmol) into rat patella tendons to investigate the effects of SP on tendons.

RESULTS

Low and high doses SP significantly enhanced the proliferation ability of TDSCs. Low-dose of SP induced the expression of tenocyte-related genes; however, high-dose of SP induced the expression of non-tenocyte genes, which was evident by the high expression of PPARγ and collagen type II. In the in vivo study, only high-doses of SP (5.0 nmol) induced the tendinosis-like changes in the patella tendon injection model. Low doses of SP (0.5 nmol) enhanced the tenogenesis compared with saline injection and the high-dose SP group.

CONCLUSIONS

SP enhances the proliferation of TDSCs in vitro and the effects of SP on tendinopathy are dose-dependent in vivo.

Comparative genomic analysis reveals occurrence of genetic recombination in virulent Cryptosporidium hominis subtypes and telomeric gene duplications in Cryptosporidium parvum

Background

Cryptosporidium hominis is a dominant species for human cryptosporidiosis. Within the species, IbA10G2 is the most virulent subtype responsible for all C. hominis–associated outbreaks in Europe and Australia, and is a dominant outbreak subtype in the United States. In recent yearsIaA28R4 is becoming a major new subtype in the United States. In this study, we sequenced the genomes of two field specimens from each of the two subtypes and conducted a comparative genomic analysis of the obtained sequences with those from the only fully sequenced Cryptosporidium parvum genome.

Results

Altogether, 8.59-9.05 Mb of Cryptosporidium sequences in 45–767 assembled contigs were obtained from the four specimens, representing 94.36-99.47% coverage of the expected genome. These genomes had complete synteny in gene organization and 96.86-97.0% and 99.72-99.83% nucleotide sequence similarities to the published genomes of C. parvum and C. hominis, respectively. Several major insertions and deletions were seen between C. hominis and C. parvum genomes, involving mostly members of multicopy gene families near telomeres. The four C. hominis genomes were highly similar to each other and divergent from the reference IaA25R3 genome in some highly polymorphic regions. Major sequence differences among the four specimens sequenced in this study were in the 5′ and 3′ ends of chromosome 6 and the gp60 region, largely the result of genetic recombination.

Conclusions

The sequence similarity among specimens of the two dominant outbreak subtypes and genetic recombination in chromosome 6, especially around the putative virulence determinant gp60 region, suggest that genetic recombination plays a potential role in the emergence of hyper-transmissible C. hominis subtypes. The high sequence conservation between C. parvum and C. hominis genomes and significant differences in copy numbers of MEDLE family secreted proteins and insulinase-like proteases indicate that telomeric gene duplications could potentially contribute to host expansion in C. parvum.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1517-1) contains supplementary material, which is available to authorized users.

Further studies on the role of dopants in LiF:Mg,Cu,Si thermoluminescent material

The 3-D thermoluminescence spectra and glow curves of LiF:Mg,Cu,Si, LiF:Mg,Cu, LiF:Mg,Si and LiF:Cu,Si with low concentrations of Mg and Cu were measured and were compared with those with high concentrations to investigate further the role of dopants in LiF:Mg,Cu,Si material. The shape of glow curves of the four samples is similar; however, LiF:Cu,Si sample had no Mg dopant. It is concluded that the TL emission to be from self-trapped excitons in LiF, and this emission could be enhanced and altered by Mg, Cu and Si dopants in LiF:Mg,Cu,Si; all three dopants are necessary to obtain the bright TL emission and may be involved in the luminescence process; Mg seems to be the most essential dopant and Cu is involved in the trapping although the role of Mg dominates; both Cu and Si play a role in the main emission process and Cu also plays a role in reducing the emission around 610 nm.

Studies on energy response of newly developed LiF:Mg,Cu,P TL chips with additional PbO doping

One of the most important characteristics of thermoluminescent detectors, if they are intended to be used in a wide range of energies, is their energy response. A comparison of the energy characteristics of the newly developed LiF:Mg,Cu,P chips with additional PbO doping (GR-200E) against GR-200A LiF:Mg,Cu,P was attempted to improve further the accuracy of personal dosimetry. Hp(10) energy response of GR-200E is quite different from that of GR-200A. For GR-200E, the anomalous energy response can be eliminated and the over-response to low-energy photons should be filtered properly. The GR-200E under the copper filter provided results within 4 % with respect to the conventional quantity value over the energy range from 65 to 1250 keV. The ratio of the Hp(10) response of the Cu-covered filters for GR-200A to that of those covered with plastic for GR-200E is a very good tool for identifying the radiation quality in the range studied. The accuracy in the dose evaluated from TLD measurements can be greatly increased.

The effects of substance P on pluripotent tendon cells: an in vitro and in vivo study

Pluripotent tendon cells (PTCs) play important roles in maintaining metabolic balance and the development of tendinopathy. Recently, substance P (SP) was identified as an important factor in the pathogenesis of tendinopathy. A better understanding of SP's effects on PTCs is essential to gain more insight into tendinopathy. This study aims to investigate the effects of SP on PTCs in vitro and in vivo. For the in vitro study, we quantified exogenous SP production by PTCs and determined the effects of SP on the proliferation and differentiation of PTCs. For the in vivo study, we used a rat patella tendon injection model to investigate the biological effects of SP on PTCs and tendons. Our results showed that exogenous SP production by PTCs was 1.80 pg/10(6) cells and SP significantly enhanced the proliferation of PTCs. Reverse transcription polymerase chain reaction (RT-PCR) results showed that SP upregulated the expression of non-tenocyte genes but downregulated the expression of tenocyte-related genes in the differentiation of PTCs. Moreover, Histological examination showed that SP induced disorganizes of tissue and tendinosis-like changes in vivo. Taken together, these findings indicate that SP enhanced PTCs' proliferation, induced non-tenocyte differentiation and plays an important role in the development of tendinopathy.

The Ellis Island Effect: A novel mobile element in a multi-drug resistant Bacteroides fragilis clinical isolate includes a mosaic of resistance genes from Gram-positive bacteria

Objectives: Bacteroides fragilis, a Gram-negative anaerobic bacterium, is alternately a gut commensal or virulent pathogen and is an important reservoir for horizontal gene transfer (HGT) of bacterial resistance and virulence genes in the human gastrointestinal tract. We identified a unique conjugative transposon (CTn) in a multidrug resistant clinical isolate of B. fragilis (BF-HMW615); we named this element CTnHyb because it included a hybrid mosaic of foreign elements. This study reports the characterization of CTnHyb and discusses the potential impact on horizontal spread of resistance genes. Results: CTnHyb contains several efflux pump genes and several genes that confer or may confer antibiotic resistance to tetracycline, kanamycin, metronidazole and spectinomycin (truncated gene). CTnHyb also contains a mosaic of mobile elements from Gram-positive organisms. CTnHyb is easily transferred from BF-HMW615 (the original isolate) to BF638R (lab strain) and integrated into the BF638R chromosome. The "foreign" (from Gram-positive bacteria) nucleotide sequences within CTnHyb were > 99% preserved indicating that the gene acquisition from the Gram-positive bacteria was very recent. Conclusion: CTnHyb is a novel CTn residing in a multidrug resistant strain of B. fragilis. The global nature and wide phylogenetic reach of HGT means that any gene in any bacterium can potentially be mobilized. Understanding the mechanisms that drive the formation and transfer of these elements and, potentially, ways to limit the transfer are necessary to prevent a devastating spread of resistance elements.

Coexistence of EGFR with KRAS, or BRAF, or PIK3CA somatic mutations in lung cancer: a comprehensive mutation profiling from 5125 Chinese cohorts

Background:

Determining the somatic mutations of epidermal growth factor receptor (EGFR)-pathway networks is the key to effective treatment for non-small cell lung cancer (NSCLC) with tyrosine kinase inhibitors (TKIs).The somatic mutation frequencies and their association with gender, smoking history and histology was analysed and reported in this study.

Methods:

Five thousand one hundred and twenty-five NSCLC patients' pathology samples were collected, and EGFR, KRAS, BRAF and PIK3CA mutations were detected by multiplex testing. The mutation status of EGFR, KRAS, BRAF and PIK3CA and their association with gender, age, smoking history and histological type were evaluated by appropriate statistical analysis.

Results:

EGFR, KRAS, BRAF and PIK3CA mutation rates revealed 36.2%, 8.4%, 0.5% and 3.3%, respectively, across the 5125 pathology samples. For the first time, evidence of KRAS mutations were detected in two female, non-smoking patients, age 5 and 14, with NSCLC. Furthermore, we identified 153 double and coexisting mutations and 7 triple mutations. Interestingly, the second drug-resistant mutations, T790M or E545K, were found in 44 samples from patients who had never received TKI treatments.

Conclusions:

EGFR exons 19, 20 and 21, and BRAF mutations tend to happen in females and non-smokers, whereas KRAS mutations were more inclined to males and smokers. Activating and resistant mutations to EGFR-TKI drugs can coexist and ‘second drug-resistant mutations', T790M or E545K, may be primary mutations in some patients. These results will help oncologists to decide candidates for mutation testing and EGFR-TKI treatment.

An overview of structure, mechanical properties, and treatment for age-related tendinopathy

Tendons transfer tensile loads from muscle to bone, which enable joint motions and stabilize joints. Tendons sustain large mechanical loads in vivo and as a result, tendons were frequently injured. Aging has been confirmed as a predisposing factor of tendinopathy and bad recovery quality following tendon repair. Current treatment methods are generally not effective and involve either symptomatic relief with non-steroidal antiinflammatory drugs and physical therapy or surgery when conservative treatments failed. The limitation in treatment options is due to our incomplete knowledge of age-related tendinopathy. Studies over the past decades have uncovered a number of important mechanical and cellular changes of aging tendon. However, the basis of aging as a major risk factor for tendon injury and impaired tendon healing remained poorly understood. The objectives of this review are to provide an overview of the current knowledge about the aging-associated changes of structure, mechanical properties and treatment in tendon and highlight causes and therapies for age-related tendinopathy.

Determining bruise etiology in muscle tissue using finite element analysis

Bruising, the result of capillary failure, is a common physical exam finding due to blunt trauma and, depending on location and severity, a potential indicator of abuse. Despite its clinical relevance, few studies have investigated the etiology of capillary failure. The goal of this study was to determine whether capillaries primarily fail under shear stress or hydraulic-induced tensile stress. An arteriole bifurcating into four capillaries was modeled using ANSYS 14.0 (®) . The capillaries were embedded in muscle tissue and a pressure of 20.4 kPa was applied. Any tensile stress exceeding 8.4 × 10(4)  Pa was considered failure. Results showed that failure occurred directly under the impact zone and where capillaries bifurcated, rather than along the line of greatest shear stress, indicating that internal tensile stress is likely the primary mode of capillary failure in bruising. These results are supported by the concept that bruising can occur via blunt trauma in which no shearing lacerations occur.

On the roles of dopants in LiF:Mg,Cu,Si thermoluminescent material

The 3D thermoluminescent spectra and glow curves of LiF:Mg,Cu,Si with various Mg, Cu and Si concentrations were measured. The shapes of the glow curves in LiF:Mg,Cu,Si, LiF:Mg,Cu and LiF:Mg,Si are similar and the glow curves have peaks at approximately the same temperatures, but with significantly different intensities. Neither the temperature of the glow peak nor the wavelength of the emission maximum changes with variation of dopants concentrations when Cu is more than 0.01 mol % in LiF:Mg,Cu,Si. The spectrum structure in LiF:Mg,Cu,Si, LiF:Mg,Cu and LiF:Mg,Si is similar in the 300-550 nm range. Some weak emissions around 610 nm are shown in LiF:Mg,Cu,Si with a Cu concentration of 0.01 mol % and in LiF:Mg,Si. It is concluded that Mg dopant mainly plays a role in the formation of trapping centres, both Cu and Si play a role in the main emission process and Cu also plays a role in reducing the emission around 610 nm.

Metastatic small-cell lung cancer presenting as fulminant hepatic failure

We report a case of a 75-year-old woman with fulminant hepatic failure due to metastatic small-cell lung cancer (SCLC). The patient was hospitalised for the management of rapidly progressive hepatic failure. Thoracic radiology identified a widened mediastinum, and prior to hospitalisation she had received antibiotics for a urinary tract infection. Consequently, her hepatic failure was deemed to be due to either sarcoidosis with hepatic involvement or an antibiotic-related adverse event and was treated with prednisolone. However, the patient's clinical condition continued to deteriorate and a liver biopsy was obtained. Histopathology and immunohistochemistry tests demonstrated almost complete parenchymal replacement with metastatic SCLC. The patient was considered to be too unwell to receive chemotherapy and hence received best supportive care instead, and died shortly thereafter.