Mapping temporo-parietal and temporo-occipital cortico-cortical connections of the human middle longitudinal fascicle in subject-specific, probabilistic, and stereotaxic Talairach spaces

Originally, the middle longitudinal fascicle (MdLF) was defined as a long association fiber tract connecting the superior temporal gyrus and temporal pole with the angular gyrus. More recently its description has been expanded to include all long postrolandic cortico-cortical association connections of the superior temporal gyrus and dorsal temporal pole with the parietal and occipital lobes. Despite its location and size, which makes MdLF one of the most prominent cerebral association fiber tracts, its discovery in humans is recent. Given the absence of a gold standard in humans for this fiber tract, its precise and complete connectivity remains to be determined with certainty. In this study using high angular resolution diffusion MRI (HARDI), we delineated for the first time, six major fiber connections of the human MdLF, four of which are temporo-parietal and two temporo-occipital, by examining morphology, topography, cortical connections, biophysical measures, volume and length in seventy brains. Considering the cortical affiliations of the different connections of MdLF we suggested that this fiber tract may be related to language, attention and integrative higher level visual and auditory processing associated functions. Furthermore, given the extensive connectivity provided to superior temporal gyrus and temporal pole with the parietal and occipital lobes, MdLF may be involved in several neurological and psychiatric conditions such as primary progressive aphasia and other aphasic syndromes, some forms of behavioral variant of frontotemporal dementia, atypical forms of Alzheimer's disease, corticobasal degeneration, schizophrenia as well as attention-deficit/hyperactivity Disorder and neglect disorders.

Volumetric Analysis from a Harmonized Multisite Brain MRI Study of a Single Subject with Multiple Sclerosis

BACKGROUND AND PURPOSE

MR imaging can be used to measure structural changes in the brains of individuals with multiple sclerosis and is essential for diagnosis, longitudinal monitoring, and therapy evaluation. The North American Imaging in Multiple Sclerosis Cooperative steering committee developed a uniform high-resolution 3T MR imaging protocol relevant to the quantification of cerebral lesions and atrophy and implemented it at 7 sites across the United States. To assess intersite variability in scan data, we imaged a volunteer with relapsing-remitting MS with a scan-rescan at each site.

MATERIALS AND METHODS

All imaging was acquired on Siemens scanners (4 Skyra, 2 Tim Trio, and 1 Verio). Expert segmentations were manually obtained for T1-hypointense and T2 (FLAIR) hyperintense lesions. Several automated lesion-detection and whole-brain, cortical, and deep gray matter volumetric pipelines were applied. Statistical analyses were conducted to assess variability across sites, as well as systematic biases in the volumetric measurements that were site-related.

RESULTS

Systematic biases due to site differences in expert-traced lesion measurements were significant (P < .01 for both T1 and T2 lesion volumes), with site explaining >90% of the variation (range, 13.0-16.4 mL in T1 and 15.9-20.1 mL in T2) in lesion volumes. Site also explained >80% of the variation in most automated volumetric measurements. Output measures clustered according to scanner models, with similar results from the Skyra versus the other 2 units.

CONCLUSIONS

Even in multicenter studies with consistent scanner field strength and manufacturer after protocol harmonization, systematic differences can lead to severe biases in volumetric analyses.

Identification and measurement of staphylococcal enterotoxin M from Staphylococcus aureus isolate associated with staphylococcal food poisoning

Staphylococcus aureus produces a wide variety of staphylococcal enterotoxins (SEs, SEA to SEX), which are responsible for staphylococcal food poisoning. This study is aimed to establish a system to detect staphylococcal enterotoxin M (SEM) protein in food matrixes. In the present study, sem gene was characterized in a S. aureus isolate H4 associated with food poisoning. The amino acid sequence of the deduced SEM protein was same as that of previously identified SEM from S. aureus 04-02981. Subsequently, mature SEM protein was expressed in Escherichia coli BL21 (DE3) cells and purified with a Ni-NTA spin column. The polyclonal and monoclonal antibody against it were prepared. Using these antibodies, a highly sensitive, specific sandwich enzyme-linked immunosorbent assay (ELISA) system was developed capable of detecting SEM in milk, meat and rice. Cross-reactivity with SEB, SEI and SEK in this method was insignificant. Quantification of SEM secretion in vitro using this novel capture ELISA revealed that SEM was mainly secreted during the transition from the exponential to the stationary phase. Furthermore, sem gene and SEM protein production were screened by PCR and the developed ELISA system. The results indicated that there were two SEM+ strains of 19 S. aureus isolates originating in cold dishes and humans suffering from food poisoning. The investigations make it possible to assess SEM in food hygiene supervision in near future.

SIGNIFICANCE AND IMPACT OF THE STUDY

Staphylococcal enterotoxins (SE) are the main causative agents of staphylococcal food poisoning. Unlike classical SEs (SEA to SEE), the relationship between newly identified SEs (SEG to SEX) and staphylococcal food poisoning has not been clearly elucidated. Recently, mild emetic potential of staphylococcal enterotoxin M (SEM) has been demonstrated, which indicated that SEM might be associated with food poisoning. However, there is currently no commercial enzyme-linked immunosorbent assay (ELISA) kit available for immunological detection of it. Therefore, we developed a highly sensitive, specific sandwich ELISA system and assayed SEM in food matrixes. This assay facilitates the study of SEM expression in vitro and in vivo. In addition, the investigations would be helpful in addressing the relative incidence of SEM+ strains in near future.

Identification and measurement of staphylococcal enterotoxin-like protein I (SEll) secretion from Staphylococcus aureus clinical isolate

AIMS

Staphylococcus aureus (Staph. aureus) produces a wide variety of staphylococcal enterotoxins (SEs) and staphylococcal enterotoxin-like (SEl) proteins, which are the most causative agents of staphylococcal food poisoning. In contrast to classical SEs (SEA to SEE), the relationship between the novel SEs/SEls (SEG to SElX) and staphylococcal food poisoning is not elucidated. This study is aimed to establish a system to detect staphylococcal enterotoxin-like protein I (SElI) for analysis of staphylococcal food poisoning.

METHODS AND RESULTS

SElI was characterized in a Staph. aureus clinical isolate associated with food poisoning; there was an amino acid substitution Thr145Ala compared to previously identified SEI from Staph. aureus 04-02981. Subsequently, SElI was expressed, purified, and the poly- and monoclonal antibodies against it were prepared. Using these antibodies, a highly sensitive sandwich enzyme-linked immunosorbent assay (ELISA) that specifically detected and measured SElI secretion from the Staph. aureus clinical isolate in LB medium, milk and bloodstream was developed.

CONCLUSIONS

The ELISA system has been successfully applied for analysing SElI secretion in vivo and in vitro.

SIGNIFICANCE AND IMPACT OF THE STUDY

The highly sensitive ELISA should make it attractive for quantifying SElI in food hygiene supervision and clinical diagnosis in near future.

Complete mitochondrial genomes from the ferns Ophioglossum californicum and Psilotum nudum are highly repetitive with the largest organellar introns

Currently, complete mitochondrial genomes (mitogenomes) are available from all major land plant lineages except ferns. Sequencing of fern mitogenomes could shed light on the major evolutionary transitions that established mitogenomic diversity among extant lineages. In this study, we generated complete mitogenomes from the adder's tongue fern (Ophioglossum californicum) and the whisk fern (Psilotum nudum). The Psilotum mitogenome (628 kb) contains a rich complement of genes and introns, some of which are the largest of any green plant organellar genome. In the Ophioglossum mitogenome (372 kb), gene and intron content is slightly reduced, including the loss of all four mitochondrial ccm genes. Transcripts of nuclear Ccm genes also were not detected, suggesting loss of the entire mitochondrial cytochrome c maturation pathway from Ophioglossum. Both fern mitogenomes are highly repetitive, yet they show extremely low levels of active recombination. Transcriptomic sequencing uncovered ˜1000 sites of C-to-U RNA editing in both species, plus a small number (< 60) of U-to-C edit sites. Overall, the first mitochondrial genomes of ferns show a mix of features shared with lycophytes and/or seed plants and several novel genomic features, enabling a robust reconstruction of the mitogenome in the common ancestor of vascular plants.

Limited mitogenomic degradation in response to a parasitic lifestyle in Orobanchaceae

In parasitic plants, the reduction in plastid genome (plastome) size and content is driven predominantly by the loss of photosynthetic genes. The first completed mitochondrial genomes (mitogenomes) from parasitic mistletoes also exhibit significant degradation, but the generality of this observation for other parasitic plants is unclear. We sequenced the complete mitogenome and plastome of the hemiparasite Castilleja paramensis (Orobanchaceae) and compared them with additional holoparasitic, hemiparasitic and nonparasitic species from Orobanchaceae. Comparative mitogenomic analysis revealed minimal gene loss among the seven Orobanchaceae species, indicating the retention of typical mitochondrial function among Orobanchaceae species. Phylogenetic analysis demonstrated that the mobile cox1 intron was acquired vertically from a nonparasitic ancestor, arguing against a role for Orobanchaceae parasites in the horizontal acquisition or distribution of this intron. The C. paramensis plastome has retained nearly all genes except for the recent pseudogenization of four subunits of the NAD(P)H dehydrogenase complex, indicating a very early stage of plastome degradation. These results lend support to the notion that loss of ndh gene function is the first step of plastome degradation in the transition to a parasitic lifestyle.

Loss of a Trans-Splicing nad1 Intron from Geraniaceae and Transfer of the Maturase Gene matR to the Nucleus in Pelargonium

The mitochondrial nad1 gene of seed plants has a complex structure, including four introns in cis or trans configurations and a maturase gene (matR) hosted within the final intron. In the geranium family (Geraniaceae), however, sequencing of representative species revealed that three of the four introns, including one in a trans configuration and another that hosts matR, were lost from the nad1 gene in their common ancestor. Despite the loss of the host intron, matR has been retained as a freestanding gene in most genera of the family, indicating that this maturase has additional functions beyond the splicing of its host intron. In the common ancestor of Pelargonium, matR was transferred to the nuclear genome, where it was split into two unlinked genes that encode either its reverse transcriptase or maturase domain. Both nuclear genes are transcribed and contain predicted mitochondrial targeting signals, suggesting that they express functional proteins that are imported into mitochondria. The nuclear localization and split domain structure of matR in the Pelargonium nuclear genome offers a unique opportunity to assess the function of these two domains using transgenic approaches.

Nickel oxide nanoparticles induced pulmonary fibrosis via TGF-β1 activation in rats

Nano nickel oxide (NiO), widely used in industry, has recently been discovered to have pulmonary toxicity. However, no subchronic exposure studies about nano NiO-induced pulmonary fibrosis have been reported. The objective of this study was to investigate pulmonary fibrosis induced by nano NiO and its potential mechanism in rats. Male Wistar rats ( n = 40, 200–240 g) were randomized into control group, nano NiO groups (0.015, 0.06, and 0.24 mg/kg), and micro NiO group (0.024 mg/kg). All rats were killed to collect lung tissue after intratracheal instillation of NiO particles twice a week for 6 weeks. To identify pulmonary fibrosis, Masson trichrome staining, hydroxyproline content, and collagen protein expression were performed. The results showed widespread lung fibrotic injury in histological examination and increased content of hydroxyproline, collagen types I and III in rat lung tissue exposed to nano NiO. To explore the potential pulmonary fibrosis mechanism, transforming growth factor beta 1 (TGF- β1) content was measured by enzyme-linked immunosorbent assay, and the messenger RNA expression of key indicators was detected by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The TGF- β1 content was increased in nano NiO exposure groups, as well as the upregulated gene expression of TGF- β1, Smad2, Smad4, matrix metalloproteinase, and tissue inhibitor of metalloproteinase. The findings indicated that nano NiO could induce pulmonary fibrosis, which may be related to TGF- β1 activation.

The Effects of Exogenous Administration of Human Coagulation Factors Following Pig-to-Baboon Liver Xenotransplantation

We sought to determine the effects of exogenous administration of human coagulation factors following pig-to-baboon liver xenotransplantation (LXT) using GalT-KO swine donors. After LXT, baboons received no coagulation factors (historical control, n = 1), bolus administration of a human prothrombin concentrate complex (hPCC; 2.5 mL/kg, n = 2), continuous infusion of hPCC (1.0 mL/h, n = 1) or continuous infusion of human recombinant factor VIIa (1 µg/kg per hour, n = 3). The historical control recipient demonstrated persistent thrombocytopenia despite platelet administration after transplant, along with widespread thrombotic microangiopathy (TMA). In contrast, platelet levels were maintained in bolus hPCC recipients; however, these animals quickly developed large-vessel thrombosis and TMA, leading to graft failure with shortened survival. Recipients of continuous coagulation factor administration experienced either stabilization or an increase in their circulating platelets with escalating doses. Furthermore, transfusion requirements were decreased, and hepatic TMA was noticeably absent in recipients of continuous coagulation factor infusions compared with the historical control and bolus hPCC recipients. This effect was most profound with a continuous, escalating dose of factor VIIa. Further studies are warranted because this regimen may allow for prolonged survival following LXT.

Evolutionary dynamics of the plastid inverted repeat: the effects of expansion, contraction, and loss on substitution rates

Rates of nucleotide substitution were previously shown to be several times slower in the plastid inverted repeat (IR) compared with single-copy (SC) regions, suggesting that the IR provides enhanced copy-correction activity. To examine the generality of this synonymous rate dependence on the IR, we compared plastomes from 69 pairs of closely related species representing 52 families of angiosperms, gymnosperms, and ferns. We explored the breadth of IR boundary shifts in land plants and demonstrate that synonymous substitution rates are, on average, 3.7 times slower in IR genes than in SC genes. In addition, genes moved from the SC into the IR exhibit lower synonymous rates consistent with other IR genes, while genes moved from the IR into the SC exhibit higher rates consistent with other SC genes. Surprisingly, however, several plastid genes from Pelargonium, Plantago, and Silene have highly accelerated synonymous rates despite their IR localization. Together, these results provide strong evidence that the duplicative nature of the IR reduces the substitution rate within this region. The anomalously fast-evolving genes in Pelargonium, Plantago, and Silene indicate localized hypermutation, potentially induced by a higher level of error-prone double-strand break repair in these regions, which generates substitutional rate variation.

Abstract P3-07-60: Impact of high SPARC expression of a primary tumor as a strong risk factor for disease recurrence and overall survival in patients with triple-negative breast cancer

Background: SPARC (secreted protein acidic and rich in cystein) is a secreted glycoprotein that interacts with extracellular matrix protein and acts as a regulator of critical cellular functions such as proliferation and cell migration. An increasing number of studies have shown altered expression of SPARC in several malignancies. However, the role of this potential biomarker in breast cancer development and progression is controversial. Triple-negative breast cancer (TNBC) is known for its poor prognosis and high recurrence probability. There is a need for prognostic biomarkers to guide treatment decisions for this subtype.

Objective: To explore the association between SPARC and the prognosis of triple-negative breast cancer.

Methods: In this study, a total of 211 samples of triple-negative breast lesions from 2004 to 2008 were collected in Cancer Hospital, Chinese Academy of Medical Sciences. SPARC expression was evaluated by immunohistochemistry using an immunoreactive score (IRS) from patients with up to 10 years clinical follow-up data. The current study set out to examine both the expression of SPARC in primary tumor tissue and to demonstrate if a link existed between the levels of SPARC and the clinical outcome. Cox proportional hazards model was used to estimate HRs and 95%CI, stratified on tumor grade, TNM stage, lymph node status and vascular invasion.

Results: High SPARC expression (IRS≥3) was observed in 52.1% of all primary tumors. Patients expressing low levels of SPARC had better disease-free survival (DFS) (HR=0.632, 95%CI:0.405-0.987, P = 0.044) as well as overall survival(OS)(HR=0.576, 95%CI:0.351-0.946, P = 0.029) compared to those with high SPARC expression levels.Furthermore, the presence of high SPARC expression was an independent prognostic factor for both DFS (HR=1.67, 95%CI:1.04-2.69, P=0.034) and OS(HR=1.77, 95%CI:1.04-3.01, P=0.037) of triple-negative breast cancer patients, stratified on tumor grade, TNM stage, lymph node metastasis and vascular invasion, with adjustment for age, hormonal status, tumor size, adjuvant radiotherapy and adjuvant chemotherapy.

Conclusion: Our results suggest that the presence of higher SPARC expression could be an indicator of high aggressiveness and may be a strong prognostic factor for triple-negative breast cancer.

Citation Format: Zhu A, Yuan P, Du F, Ding X, Xu B. Impact of high SPARC expression of a primary tumor as a strong risk factor for disease recurrence and overall survival in patients with triple-negative breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P3-07-60.

Dynamic evolution of Geranium mitochondrial genomes through multiple horizontal and intracellular gene transfers

The exchange of genetic material between cellular organelles through intracellular gene transfer (IGT) or between species by horizontal gene transfer (HGT) has played an important role in plant mitochondrial genome evolution. The mitochondrial genomes of Geraniaceae display a number of unusual phenomena including highly accelerated rates of synonymous substitutions, extensive gene loss and reduction in RNA editing. Mitochondrial DNA sequences assembled for 17 species of Geranium revealed substantial reduction in gene and intron content relative to the ancestor of the Geranium lineage. Comparative analyses of nuclear transcriptome data suggest that a number of these sequences have been functionally relocated to the nucleus via IGT. Evidence for rampant HGT was detected in several Geranium species containing foreign organellar DNA from diverse eudicots, including many transfers from parasitic plants. One lineage has experienced multiple, independent HGT episodes, many of which occurred within the past 5.5 Myr. Both duplicative and recapture HGT were documented in Geranium lineages. The mitochondrial genome of Geranium brycei contains at least four independent HGT tracts that are absent in its nearest relative. Furthermore, G. brycei mitochondria carry two copies of the cox1 gene that differ in intron content, providing insight into contrasting hypotheses on cox1 intron evolution.

Network analysis of postharvest senescence process in citrus fruits revealed by transcriptomic and metabolomic profiling

Citrus (Citrus spp.), a nonclimacteric fruit, is one of the most important fruit crops in global fruit industry. However, the biological behavior of citrus fruit ripening and postharvest senescence remains unclear. To better understand the senescence process of citrus fruit, we analyzed data sets from commercial microarrays, gas chromatography-mass spectrometry, and liquid chromatography-mass spectrometry and validated physiological quality detection of four main varieties in the genus Citrus. Network-based approaches of data mining and modeling were used to investigate complex molecular processes in citrus. The Citrus Metabolic Pathway Network and correlation networks were constructed to explore the modules and relationships of the functional genes/metabolites. We found that the different flesh-rind transport of nutrients and water due to the anatomic structural differences among citrus varieties might be an important factor that influences fruit senescence behavior. We then modeled and verified the citrus senescence process. As fruit rind is exposed directly to the environment, which results in energy expenditure in response to biotic and abiotic stresses, nutrients are exported from flesh to rind to maintain the activity of the whole fruit. The depletion of internal substances causes abiotic stresses, which further induces phytohormone reactions, transcription factor regulation, and a series of physiological and biochemical reactions.