Microbial characterization based on multifractal analysis of metagenomes

IntroductionThe species diversity of microbiomes is a cutting-edge concept in metagenomic research. In this study, we propose a multifractal analysis for metagenomic research.Method and ResultsFirstly, we visualized the chaotic game representation (CGR) of simulated metagenomes and real metagenomes. We find that metagenomes are visualized with self-similarity. Then we defined and calculated the multifractal dimension for the visualized plot of simulated and real metagenomes, respectively. By analyzing the Pearson correlation coefficients between the multifractal dimension and the traditional species diversity index, we obtain that the correlation coefficients between the multifractal dimension and the species richness index and Shannon diversity index reached the maximum value when q = 0, 1, and the correlation coefficient between the multifractal dimension and the Simpson diversity index reached the maximum value when q = 5. Finally, we apply our method to real metagenomes of the gut microbiota of 100 infants who are newborn and 4 and 12 months old. The results show that the multifractal dimensions of an infant's gut microbiomes can distinguish age differences.Conclusion and DiscussionThere is self-similarity among the CGRs of WGS of metagenomes, and the multifractal spectrum is an important characteristic for metagenomes. The traditional diversity indicators can be unified under the framework of multifractal analysis. These results coincided with similar results in macrobial ecology. The multifractal spectrum of infants’ gut microbiomes are related to the development of the infants

Chlorido(1,10-phenanthroline)(1H-1,2,4-triazole-3-carboxyl­ato)copper(II)

The title complex, [Cu(C3H2N3O2)Cl(C12H8N2)], crystallizes with two independent mol­ecules in the asymmetric unit. Each CuII atom is coordinated by an N atom and an O atom from the bidentate 1H-1,2,4-triazole-3-carboxyl­ate ligand, two N atoms from the 1,10-phenanthroline ligand, and the Cl atom. The coordination geometry is based on a ClN3O square pyramid. In the crystal structure, the mol­ecules are linked by inter­molecular N—H⋯O hydrogen bonds

Sclerosing mesenteritis as a rare cause of abdominal pain and intraabdominal mass: a cases report and review of the literature

Sclerosing mesenteritis is a rare, benign, and chronic fibrosing inflammation disease with unknown etiology that affects the mesentery of small bowel and colon. The disease has two well-established histological types: the acute or subacute form known as mesenteric panniculitis and the chronic form known as retractile or sclerosing mesenteritis. Because the sclerosing mesenteritis is lack of special clinical manifestation and typical signs, so the patients are very easy to be misdiagnosed. The correct diagnosis of sclerosing mesenteritis depends on pathological examination and exploratory laparotomy. We report a case of sclerosing mesenteritis in a 52-year-old male who presented with chronic abdominal pain and intraabdominal mass. This patient had a long-term and heavy drinking history. He was misdiagnosed as celiac teratoma by CT examination and then underwent an exploratory laparotomy at March 2 2004. A mass, its diameter being about 5 cm, was detected in mesentery of distal ileum. Although a few small intestines tightly adhered on the mass, the involved intestine had no obstruction. The intraoperative biopsy indicated that it was an inflammatory mass. The mass and adhered intestines were removed. He was diagnosed with sclerosing mesenteritis by histopathological examination of paraffin section. After operation, this patient went well and lives without recrudescence at the time we wrote this paper

Backbone phylogeny and adaptive evolution of Pleurospermum s. l.: New insights from phylogenomic analyses of complete plastome data

Pleurospermum is a taxonomically challenging taxon of Apiaceae, as its circumscription and composition remain controversial for morphological similarities with several related genera, leading to a dispute between Pleurospermum in the broad sense and strict sense. While evidence from previous molecular studies recognized plural branching lineages within the Pleurospermum s. l., it did not support the latest delimitation of Pleurospermum s. str. by only two closely related northern species. So far, no proper delimitation for Pleurospermum has come up, and many of the plural taxa in Pleurospermum s. l. remain unresolved, which may be due to poor phylogenetic resolution yielded barely from ITS sequences. Herein, we newly assembled 40 complete plastomes from 36 species of Pleurospermum s. l. and related genera, 34 of which were first reported and generated a well-resolved backbone phylogeny in a framework of the subfamily Apioideae. From the phylogeny with greatly improved resolution, a total of six well-supported monophyletic lineages within Pleurospermum s. l. were recognized falling in different major clades of Apioideae. Combining morphological characteristics with phylogenetic inference, we suggested to re-delimit the Pleurospermum s. str. by introducing nine species mainly from the Himalayan regions and proposed its boundary features; the remaining species were suggested to be excluded from Pleurospermum to incorporate into their more related taxa being revealed. On this basis, the plastome comparison revealed not only the high conservatism but also the mild differences among lineages in plastome structure and gene evolution. Overall, our study provided a backbone phylogeny essential for further studies of the taxonomically difficult taxa within Pleurospermum s. l

Phase I Trial of Escalating-dose Cisplatin with 5-fluorouracil and Concurrent Radiotherapy in Chinese Patients with Esophageal Cancer

We defined the maximum-tolerated dose (MTD) of chemoradiotherapy (cisplatin (CDDP) with 5-fluorouracil (5-FU) and concurrent chemoradiotherapy) for Chinese patients with esophageal cancer. Twenty-one previously untreated patients with primary esophageal cancer were entered into this study. Escalating doses of CDDP with 5-FU were administered in a modified Fibonacci sequence, with concurrent conventional fractionation radiotherapy (CFR) of 60 Gy or 50 Gy. The starting doses were CDDP 37.5 mg/m2 on day 1, and 5-FU 500 mg/m2 on days 1-5, respectively. The regimen was repeated 4 times every 28 days. If no dose-limiting toxicity (DLT) was observed, the next dose level was applied. The procedures were repeated until DLT appeared. The MTD was declared to be 1 dose level below the level at which DLT appeared. DLT was grade 3 radiation-induced esophagitis at a dose level of CDDP 60 mg/m2 with 5-FU 700 mg/m2 and concurrent 60 Gy CFR. MTD was defined as CDDP 52.5 mg/m2 with 5-FU 700 mg/m2 and concurrent 50 Gy CFR. The MTD of CDDP with 5-FU and in concurrent chemoradiotherapy for Chinese patients with esophageal cancer is CDDP 52.5 mg/m2 on day 1 and 5FU 700 mg/m2 on days 1-5, repeated 4 times every 28 days, and concurrent 50 Gy CFR. Further evaluation of this regimen in a prospective phase II trial is ongoing.</p

Identification and characterization of microRNAs in Clonorchis sinensis of human health significance

<p>Abstract</p> <p>Background</p> <p><it>Clonorchis sinensis </it>is a zoonotic parasite causing clonorchiasis-associated human disease such as biliary calculi, cholecystitis, liver cirrhosis, and it is currently classified as carcinogenic to humans for cholangiocarcinoma. MicroRNAs (miRNAs) are non-coding, regulating small RNA molecules which are essential for the complex life cycles of parasites and are involved in parasitic infections. To identify and characterize miRNAs expressed in adult <it>C. sinensis </it>residing chronically in the biliary tract, we developed an integrative approach combining deep sequencing and bioinformatic predictions with stem-loop real-time PCR analysis.</p> <p>Results</p> <p>Here we report the use of this approach to identify and clone 6 new and 62,512 conserved <it>C. sinensis </it>miRNAs which belonged to 284 families. There was strong bias on families, family members and sequence nucleotides in <it>C. sinensis</it>. Uracil was the dominant nucleotide, particularly at positions 1, 14 and 22, which were located approximately at the beginning, middle and end of conserved miRNAs. There was no significant "seed region" at the first and ninth positions which were commonly found in human, animals and plants. Categorization of conserved miRNAs indicated that miRNAs of <it>C. sinensis </it>were still innovated and concentrated along three branches of the phylogenetic tree leading to bilaterians, insects and coelomates. There were two miRNA strategies in <it>C. sinensis </it>for its parasitic life: keeping a large category of miRNA families of different animals and keeping stringent conserved seed regions with high active innovation in other places of miRNAs mainly in the middle and the end, which were perfect for the parasite to perform its complex life style and for host changes.</p> <p>Conclusions</p> <p>The present study represented the first large scale characterization of <it>C. sinensis </it>miRNAs, which have implications for understanding the complex biology of this zoonotic parasite, as well as miRNA studies of other related species such as <it>Opisthorchis viverrini </it>and <it>Opisthorchis felineus </it>of human and animal health significance.</p