RNA-seq of peripheral blood mononuclear cells of congenital generalized lipodystrophy type 2 patients.

Illumina RNA-seq analysis was used to characterize the whole transcriptomes of peripheral blood mononuclear cells (PBMCs) from patients with congenital generalized lipodystrophy. RNA-seq information for seven patients with type 2 congenital generalized lipodystrophy (CGL2; Berardinelli-Seip congenital lipodystrophy, BSCL2) was obtained and compared with similar information for seven age- and sex-matched healthy control subjects. All seven CGL2 patients carried biallelic pathogenic mutations affecting the BSCL2 gene and had clinical symptoms of varying severity. The findings provide the whole-transcriptome signatures of PBMCs of CGL2 patients, allowing further exploration of gene expression patterns/signatures associated with the various clinical symptoms of patients with this disease.

Comprehensive Cohort Analysis of Mutational Spectrum in Early Onset Breast Cancer Patients.

Early onset breast cancer (EOBC), diagnosed at age ~40 or younger, is associated with a poorer prognosis and higher mortality rate compared to breast cancer diagnosed at age 50 or older. EOBC poses a serious threat to public health and requires in-depth investigation. We studied a cohort comprising 90 Taiwanese female patients, aiming to unravel the underlying mechanisms of EOBC etiopathogenesis. Sequence data generated by whole-exome sequencing (WES) and whole-genome sequencing (WGS) from white blood cell (WBC)-tumor pairs were analyzed to identify somatic missense mutations, copy number variations (CNVs) and germline missense mutations. Similar to regular breast cancer, the key somatic mutation-susceptibility genes of EOBC include TP53 (40% prevalence), PIK3CA (37%), GATA3 (17%) and KMT2C (17%), which are frequently reported in breast cancer; however, the structural protein-coding genes MUC17 (19%), FLG (16%) and NEBL (11%) show a significantly higher prevalence in EOBC. Furthermore, the top 2 genes harboring EOBC germline mutations, MUC16 (19%) and KRT18 (19%), encode structural proteins. Compared to conventional breast cancer, an unexpectedly higher number of EOBC susceptibility genes encode structural proteins. We suspect that mutations in structural proteins may increase physical permeability to environmental hormones and carcinogens and cause breast cancer to occur at a young age.

Proteogenomics of Non-smoking Lung Cancer in East Asia Delineates Molecular Signatures of Pathogenesis and Progression.

Lung cancer in East Asia is characterized by a high percentage of never-smokers, early onset and predominant EGFR mutations. To illuminate the molecular phenotype of this demographically distinct disease, we performed a deep comprehensive proteogenomic study on a prospectively collected cohort in Taiwan, representing early stage, predominantly female, non-smoking lung adenocarcinoma. Integrated genomic, proteomic, and phosphoproteomic analysis delineated the demographically distinct molecular attributes and hallmarks of tumor progression. Mutational signature analysis revealed age- and gender-related mutagenesis mechanisms, characterized by high prevalence of APOBEC mutational signature in younger females and over-representation of environmental carcinogen-like mutational signatures in older females. A proteomics-informed classification distinguished the clinical characteristics of early stage patients with EGFR mutations. Furthermore, integrated protein network analysis revealed the cellular remodeling underpinning clinical trajectories and nominated candidate biomarkers for patient stratification and therapeutic intervention. This multi-omic molecular architecture may help develop strategies for management of early stage never-smoker lung adenocarcinoma.

Enhanced diuron remediation by microorganism-immobilized silkworm excrement composites and their impact on soil microbial communities.

In response to the potential threats stemming from the constantly increasing consumption of herbicides, bioremediation offers a beneficial technology for reducing the widespread herbicide contamination. In order to facilitate the in-situ degradation of diuron, Arthrobacter globiformis D47 is captured onto a biocompatible carrier to assemble the microorganism-immobilized silkworm excrement (MSE) composites. By characterization, bacterial cells are intensively entrapped in/onto the carriers, showing high survival and stable catalytic degradation of target pollutants. Meanwhile, MES composites display excellent adaptiveness and feasibility under different conditions, and the average half-life of diuron is shortened to 7.69 d in sugarcane field where diuron is regularly sprayed for weed management. Importantly, we assess that the use of MSE may generally boost the overall xenobiotic-degrading ability, likely due to the slight alternation of the diversity and composition of soil microbial communities. Taking together, the presented MSE provides an attractive in situ approach for the efficient diuron removal as well as for the more feasible utilization of various pollutant-degrading microorganisms.

Analysis of microbial sequences in plasma cell-free DNA for early-onset breast cancer patients and healthy females.

BACKGROUND: Cell-free circulating DNA (cfDNA) is becoming a useful biopsy for noninvasive diagnosis of diseases. Microbial sequences in plasma cfDNA may provide important information to improve prognosis and treatment. We have developed a stringent method to identify microbial species via microbial cfDNA in the blood plasma of early-onset breast cancer (EOBC) patients and healthy females. Empirically, microbe-originated sequence reads were identified by mapping non-human PE reads in cfDNA libraries to microbial databases. Those mapped concordantly to unique microbial species were assembled into contigs, which were subsequently aligned to the same databases. Microbial species uniquely aligned were identified and compared across all individuals on MCRPM (Microbial CfDNA Reads Per Million quality PE reads) basis. RESULTS: The predominant microbial cfDNAs in all plasma samples examined are originated from bacteria and these bacteria were limited to only a few genera. Among those, Acinetobacter johnsonii XBB1 and low levels of Mycobacterium spp. were commonly found in all healthy females, but also present in an EOBC patient. Compared to those in healthy counterparts, bacterial species in EOBC patients are more diverse and more likely to present at high levels. Among these three EOBC patients tested, a patient who has record high titer (2,724 MCRPM) of Pseudomonas mendocina together with 8.82 MCRPM of Pannonibacter phragmitetus has passed away; another patient infected by multiple Sphingomonas species remains alive; while the third patient who has similar microbial species (Acinetobacter johnsonii XBB1) commonly seen in normal controls is having a normal life. CONCLUSIONS: Our preliminary data on the profiles of microbial cfDNA sequences suggested that it may have some prognostic value in cancer patients. Validation in larger number of patients is warranted.

Gene-to-Gene Network Analysis of the Mediation of Plant Innate Immunity by the Eliciting Plant Response-Like 1 (Epl1) Elicitor of Trichoderma formosa.

A new clade, Trichoderma formosa, secretes eliciting plant response-like 1 (Epl1), a small peptide elicitor that stimulates plant immunity. Nicotiana benthamiana pretreated with Epl1 for 3 days developed immunity against Tomato mosaic virus (ToMV) infection. The transcriptome profiles of T. formosa and N. benthamiana were obtained by deep sequencing; the transcript of Epl1 is 736 nt in length and encodes a 12-kDa peptide. Identifying critical genes in Epl1-mediated immunity was challenging due to high similarity between the transcriptome expression profiles of Epl1-treated and ToMV-infected N. benthamiana samples. Therefore, an efficient bioinformatics data mining approach was used for high-throughput transcriptomic assays in this study. We integrated gene-to-gene network analysis into the ContigViews transcriptome database, and genes related to jasmonic acid and ethylene signaling, salicylic acid signaling, leucine-rich repeats, transcription factors, and histone variants were hubs in the gene-to-gene networks. In this study, the Epl1 of T. formosa triggers plant immunity against various pathogen infections. Moreover, we demonstrated that high-throughput data mining and gene-to-gene network analysis can be used to identify critical candidate genes for further studies on the mechanisms of plant immunity.

Complete Taiwanese Macaque (Macaca cyclopis) Mitochondrial Genome: Reference-Assisted de novo Assembly with Multiple k-mer Strategy.

The Taiwanese (Formosan) macaque (Macaca cyclopis) is the only nonhuman primate endemic to Taiwan. This primate species is valuable for evolutionary studies and as subjects in medical research. However, only partial fragments of the mitochondrial genome (mitogenome) of this primate species have been sequenced, not mentioning its nuclear genome. We employed next-generation sequencing to generate 2 x 90 bp paired-end reads, followed by reference-assisted de novo assembly with multiple k-mer strategy to characterize the M. cyclopis mitogenome. We compared the assembled mitogenome with that of other macaque species for phylogenetic analysis. Our results show that, the M. cyclopis mitogenome consists of 16,563 nucleotides encoding for 13 protein-coding genes, 2 ribosomal RNAs and 22 transfer RNAs. Phylogenetic analysis indicates that M. cyclopis is most closely related to M. mulatta lasiota (Chinese rhesus macaque), supporting the notion of Asia-continental origin of M. cyclopis proposed in previous studies based on partial mitochondrial sequences. Our work presents a novel approach for assembling a mitogenome that utilizes the capabilities of de novo genome assembly with assistance of a reference genome. The availability of the complete Taiwanese macaque mitogenome will facilitate the study of primate evolution and the characterization of genetic variations for the potential usage of this species as a non-human primate model for medical research.

Correlation of renal ultrasonographic findings with inflammatory volume from dimercaptosuccinic acid renal scans in children with acute pyelonephritis.

PURPOSE: We correlated abnormal findings on renal ultrasonography (US) and inflammatory volume (Volume) on technetium dimercaptosuccinic acid renal single photon emission computerized tomography (DMSA) in children with acute pyelonephritis (APN) with renal scars. MATERIALS AND METHODS: A total of 31 males and 14 females (9 days to 9.8 years old) who fulfilled diagnostic criteria for APN and who underwent initial DMSA between January 1995 and July 2002 and followup DMSA at least 6 months later were enrolled in the study. APN was diagnosed by initial DMSA, and placement in the scar or scar-free group was determined by followup DMSA. Photopenic areas on initial DMSA were calculated as Volume, and were compared to US findings. RESULTS: Ultrasound demonstrated 35 abnormal kidneys (38.9%) among these children with APN. Significant differences in age, Volume (11.19 +/- 2.52 ml vs 3.02 +/- 0.75 ml, p <0.005), C-reactive protein (CRP) and photopenic lesion on initial DMSA were found between children with abnormal and normal US. Of 65 children with initial APN foci 33 (50.8%) recovered, and the others had development of scars. The sensitivity of US for detecting APN (identified by DMSA scan) was 49.2%, and the specificity was 88% (OR 7.1, 95% CI 2.18 to 24.41). The sensitivity of US for predicting renal scarring was 59.4%, and the specificity was 60.6% (OR 2.3, 95% CI 0.82 to 7.65). Patients with abnormal US findings and high serum CRP (greater than 70 mg/l) had a large Volume (10.96 +/- 3.05 ml) and a 76.2% chance of being in the scar group. CONCLUSIONS: US findings are significantly correlated to Volume in APN. Along with a high level of CRP, US is helpful in predicting development of renal scarring.

Renal abscess in children: a clinical retrospective study.

A renal abscess is rare in children and diagnosis is not readily apparent before hospitalization, because symptoms are often insidious and nonspecific. To evaluate the diagnostics and therapy of renal abscess in the pediatric group, we will report eight cases of renal abscess in children to illustrate the variable features of this condition. Eight patients, 6 to 156 (mean, 45.9) months old, with renal abscesses in 9 kidneys were identified. Ultrasound and computed tomography proved to be the most valuable diagnostic tool, revealing a hypoechoic or hypodense mass. Fever, abdominal pain, and leukocytosis were common presenting features, but no child presented symptoms of loin pain. Escherichia coli was identified in the urine culture among the 6 cases and blood culture in one case. Three children were associated with mild to moderate vesicoureteral reflux. All patients had an intensive antibiotic treatment, which led to resolution of the abscess in eight of the nine kidneys. In one case, the abscess had to be drained using the CT-guided percutaneous drainage. During follow-up, seven children received 99mTc DMSA renal SPECT and only two of them had complete remission without sequelae of renal scar. We concluded that the renal abscesses must be assumed, especially, in children with prolonged fever, abdominal pain, and a high value of CRP. Ultrasonography is just a screening test to detect renal swelling, bulging, and enlargement; however, a CT scan is more sensitive and can detect abscess formation, as well as define the extent of the disease for planning conservative antibiotic treatment or additional drainage. Finally, DMSA renal SPECT is the best and the most sensitive examination for detecting the extension area of renal inflammation and correlated with the renal outcome.

Acute pyelonephritis and sequelae of renal scar in pediatric first febrile urinary tract infection.

To investigate the incidence of acute pyelonephritis (APN) and renal scarring in children with febrile urinary tract infection (UTI), 191 of 216 (88%) children with their first episode of UTI received (99m)Tc-dimercaptosuccinic acid renal single-photon emission computed tomography. They were investigated within 7 days of admission and were followed for 6 months. One hundred and six patients (49.1%) underwent a voiding cystourethrogram. The incidence of vesicoureteric reflux (VUR) in group I (