Panoramic insights into microevolution and macroevolution of a Prevotella copri-containing lineage in primate guts

Prevotella copri and its related taxa are widely detected in mammalian gut microbiomes and have been linked with an enterotype in humans. However, their microevolution and macroevolution among hosts are poorly characterized. In this study, extensively collected marker genes and genomes were analyzed to trace their evolutionary history, host specificity, and biogeographic distribution. Investigations based on marker genes and genomes suggest that a P. copri-containing lineage (PCL) harbors diverse species in higher primates. Firstly, P. copri in the human gut consisted of multiple groups exhibiting high genomic divergence and conspicuous but non-strict biogeographic patterns. Most African strains with high genomic divergence from other strains were phylogenetically located at the root of the species, indicating the co-evolutionary history of P. copri and Homo sapiens. Secondly, although long-term co-evolution between PCL and higher primates was revealed, sporadic signals of co-speciation and extensive host jumping of PCL members were suggested among higher primates. Metagenomic and phylogenetic analyses indicated that P. copri and other PCL species found in domesticated mammals had been recently transmitted from humans. Thirdly, strong evidence was found on the extensively horizontal transfer of genes (e.g., genes encoding carbohydrate-active enzymes) among sympatric P. copri groups and PCL species in the same primate host. Our study provides panoramic insights into the combined effects of vertical and horizontal transmission, as well as potential niche adaptation, on the microevolutionary and macroevolutionary history for an enterotype-representative lineage

You Do (Not) Belong Here: Detecting DPI Evasion Attacks with Context Learning

As Deep Packet Inspection (DPI) middleboxes become increasingly popular, a spectrum of adversarial attacks have emerged with the goal of evading such middleboxes. Many of these attacks exploit discrepancies between the middlebox network protocol implementations, and the more rigorous/complete versions implemented at end hosts. These evasion attacks largely involve subtle manipulations of packets to cause different behaviours at DPI and end hosts, to cloak malicious network traffic that is otherwise detectable. With recent automated discovery, it has become prohibitively challenging to manually curate rules for detecting these manipulations. In this work, we propose CLAP, the first fully-automated, unsupervised ML solution to accurately detect and localize DPI evasion attacks. By learning what we call the packet context, which essentially captures inter-relationships across both (1) different packets in a connection; and (2) different header fields within each packet, from benign traffic traces only, CLAP can detect and pinpoint packets that violate the benign packet contexts (which are the ones that are specially crafted for evasion purposes). Our evaluations with 73 state-of-the-art DPI evasion attacks show that CLAP achieves an Area Under the Receiver Operating Characteristic Curve (AUC-ROC) of 0.963, an Equal Error Rate (EER) of only 0.061 in detection, and an accuracy of 94.6% in localization. These results suggest that CLAP can be a promising tool for thwarting DPI evasion attacks.Comment: 12 pages, 12 figures; accepted to ACM CoNEXT 202

a practical tool to implement hospital-based syndromic surveillance: SCM

Background: syndromic surveillance has been widely used for the early warning of infectious disease outbreaks, especially in mass gatherings, but the collection of electronic data on symptoms in hospitals is one of the fundamental challenges that must be overcome during operating a syndromic surveillance system. The objective of our study is to describe and evaluate the implementation of a symptom-clicking-module (SCM) as a part of the enhanced hospital-based syndromic surveillance during the 41st World Exposition in Shanghai, China, 2010.Methods: the SCM, including 25 targeted symptoms, was embedded in the sentinels’ Hospital Information Systems (HIS). The clinicians used SCM to record these information of all the visiting patients, and data were collated and transmitted automatically in daily batches. The symptoms were categorized into seven targeted syndromes using pre-defined criteria, and statistical algorithms were applied to detect temporal aberrations in the data series.Results: SCM was deployed successfully in each sentinel hospital and was operated during the 184-day surveillance period. A total of 1,730,797 patient encounters were recorded by SCM, and 6.1 % (105,352 visits) met the criteria of the seven targeted syndromes. Acute respiratory and gastrointestinal syndromes were reported most frequently, accounted for 92.1 % of reports in all syndromes, and the aggregated time-series presented an obvious day-of-week variation over the study period. In total, 191 aberration signals were triggered, and none of them were identified as outbreaks after verification and field investigation.Conclusions: SCM has acted as a practical tool for recording symptoms in the hospital-based enhanced syndromic surveillance system during the 41st World Exposition in Shanghai, in the context of without a preexisting electronic tool to collect syndromic data in the HIS of the sentinel hospitals

Therapeutic Effects of Chinese Medicine Herb Pair, Huzhang and Guizhi, on Monosodium Urate Crystal-Induced Gouty Arthritis in Rats Revealed by Anti-Inflammatory Assessments and NMR-Based Metabonomics

The present study was undertaken to evaluate the therapeutic effects of Huzhang-Guizhi herb pair (HG), firstly included in Hu-Zhang Power documented in Taiping Shenghui Fang, on monosodium urate (MSU) crystals-induced gouty arthritis in rats. We found that pretreatment with HG in rats with gouty arthritis could significantly attenuate the ankle joint swelling, and this beneficial antigout effect might be mediated, at least in part, by inhibiting tumor necrosis factor-alpha (TNF-α) and interleukin-1 beta (IL-1β) production in synovial fluid as well as nuclear transcription factor-κB p65 (NF-κB p65) protein expression in synovial tissue. Moreover, metabonomic analysis demonstrated that 5 and 6 potential biomarkers associated with gouty arthritis in plasma and urine, respectively, which were mainly involved in energy metabolism, amino acid metabolism, and gut microbe metabolism, were identified. HG could reverse the pathological process of MSU-induced gouty arthritis through regulating the disturbed metabolic pathways. These results provided important mechanistic insights into the protective effects of HG against MSU-induced gouty arthritis in rats

Comparative study of the reproductive biology of two congeneric and introduced goby species: implications for management strategies

A full understanding of life history characteristics of invasive species is a fundamental prerequisite for the development of management strategies. Two introduced goby species (Rhinogobius cliffordpopei and Rhinogobius giurinus) have established highly abundant populations in Lake Erhai (China). In the present study, we examined the reproductive biology of these two species with the aim of improving the efficiency of management strategy. The results indicated that R. cliffordpopei spawned from February to June, whereas R. giurinus spawned from April to August. Rhinogobius cliffordpopei showed higher gonado-somatic indices and had larger eggs than R. giurinus. The adult sex ratio of R. cliffordpopei was female skewed, but that of R. giurinus was equal. Rhinogobius cliffordpopei showed a male-skewed sexual size dimorphism, whereas the body size of R. giurinus varied only slightly between males and females. The different reproductive traits appear as a crucial biologic aspect for developing control programs. Specifically, control measures should be implemented and/or intensified from September to February for R. cliffordpopei and from January to April for R. giurinus. The body size of the smaller R. cliffordpopei females is the determinant for minimal mesh size of the nets used in physical removals of R. cliffordpopei.A full understanding of life history characteristics of invasive species is a fundamental prerequisite for the development of management strategies. Two introduced goby species (Rhinogobius cliffordpopei and Rhinogobius giurinus) have established highly abundant populations in Lake Erhai (China). In the present study, we examined the reproductive biology of these two species with the aim of improving the efficiency of management strategy. The results indicated that R. cliffordpopei spawned from February to June, whereas R. giurinus spawned from April to August. Rhinogobius cliffordpopei showed higher gonado-somatic indices and had larger eggs than R. giurinus. The adult sex ratio of R. cliffordpopei was female skewed, but that of R. giurinus was equal. Rhinogobius cliffordpopei showed a male-skewed sexual size dimorphism, whereas the body size of R. giurinus varied only slightly between males and females. The different reproductive traits appear as a crucial biologic aspect for developing control programs. Specifically, control measures should be implemented and/or intensified from September to February for R. cliffordpopei and from January to April for R. giurinus. The body size of the smaller R. cliffordpopei females is the determinant for minimal mesh size of the nets used in physical removals of R. cliffordpopei

The BMP inhibitor follistatin-like 1 (FSTL1) suppresses cervical carcinogenesis

Follistatin-like 1 (FSTL1) is a cancer-related matricellular secretory protein with contradictory organ-specific roles. Its contribution to the pathogenesis of cervical carcinoma is still not clear. Meanwhile, it is necessary to identify novel candidate genes to understand cervical carcinoma’s pathogenesis further and find potential therapeutic targets. We collected cervical carcinoma samples and matched adjacent tissues from patients with the locally-advanced disease and used cervical carcinoma cell lines HeLa and C33A to evaluate the effects of FSTL1 on CC cells. The mRNA transcription and protein expression of FSTL1 in cervical carcinoma tumor biopsy tissues were lower than those of matched adjacent tissues. Patients with a lower ratio of FSTL1 mRNA between the tumor and its matched adjacent tissues showed a correlation with the advanced cervical carcinoma FIGO stages. High expression of FSTL1 markedly inhibited the proliferation, motility, and invasion of HeLa and C33A. Regarding mechanism, FSTL1 plays its role by negatively regulating the BMP4/Smad1/5/9 signaling. Our study has demonstrated the tumor suppressor effect of FSTL1, and these findings suggested a potential therapeutic target and biomarker for cervical carcinoma

Status and historical changes in the fish community in Erhai Lake

Erhai Lake is the second largest freshwater lake on the Yunnan Plateau, Southwest China. In recent decades, a number of exotic fish species have been introduced into the lake and the fish community has changed considerably. We evaluated the status of the fish community based on surveys with multimesh gillnet, trap net, and benthic fyke-net between May 2009 and April 2012. In addition, we evaluated the change in the community using historical data (1952-2010) describing the fish community and fishery harvest. The current fish community is dominated by small-sized fishes, including Pseudorasbora parva, Rhinogobius giurinus, Micropercops swinhonis, Hemiculter leucisculus, and Rhinogobius cliffordpopei. These accounted for 87.7% of the 22 546 total specimens collected. Omnivorous and carnivorous species dominated the community. A canonical correspondence analysis (CCA) plot revealed that the distribution of fishes in the lake is influenced by aquatic plants, water temperature, pH, and season. The abundance of indigenous species has declined sharply, and a majority of endemic species have been extirpated from the lake (a decrease from seven to two species). In contrast, the number of exotic species has increased since the 1960s to a total of 22 at present. The fishery harvest decreased initially following the 1960s, but has since increased due to the introduction of non-native fish and stocking of native fish. The fishery harvest was significantly correlated with total nitrogen, not total phosphorus, during the past 20 years. Based on our results, we discuss recommendations for the restoration and conservation of the fish resources in Erhai Lake.Erhai Lake is the second largest freshwater lake on the Yunnan Plateau, Southwest China. In recent decades, a number of exotic fish species have been introduced into the lake and the fish community has changed considerably. We evaluated the status of the fish community based on surveys with multimesh gillnet, trap net, and benthic fyke-net between May 2009 and April 2012. In addition, we evaluated the change in the community using historical data (1952-2010) describing the fish community and fishery harvest. The current fish community is dominated by small-sized fishes, including Pseudorasbora parva, Rhinogobius giurinus, Micropercops swinhonis, Hemiculter leucisculus, and Rhinogobius cliffordpopei. These accounted for 87.7% of the 22 546 total specimens collected. Omnivorous and carnivorous species dominated the community. A canonical correspondence analysis (CCA) plot revealed that the distribution of fishes in the lake is influenced by aquatic plants, water temperature, pH, and season. The abundance of indigenous species has declined sharply, and a majority of endemic species have been extirpated from the lake (a decrease from seven to two species). In contrast, the number of exotic species has increased since the 1960s to a total of 22 at present. The fishery harvest decreased initially following the 1960s, but has since increased due to the introduction of non-native fish and stocking of native fish. The fishery harvest was significantly correlated with total nitrogen, not total phosphorus, during the past 20 years. Based on our results, we discuss recommendations for the restoration and conservation of the fish resources in Erhai Lake

Habitat segregation between two congeneric and introduced goby species

Spatial segregation is one of the most important mechanisms that facilitates coexistence among competing species. Large populations of two introduced and congeneric goby species (Rhinogobius giurinus and Rhinogobius cliffordpopei) now co-occur in Lake Erhai, a plateau lake in the Yunnan-Guizhou Plateau (China). Herein we quantified the spatio-temporal distribution of the two species to determine whether spatial segregation occurred within the same ecosystem. A total of 67,819 individuals of R. giurinus and 36,043 of R. cliffordpopei were sampled across four seasons. The results indicated that R. giurinus mostly occupied profundal habitat (PH) while R. cliffordpopei mainly used littoral habitat (LH). Correlation analysis revealed the abundance of R. giurinus was positively associated with deep water, silt and coarse sand substrata, whereas the distribution of R. cliffordpopei was positively associated with high densities of macrozooplanktons and high abundances of other fish species, high concentration of dissolved oxygen and high densities of submerged macrophytes. Except in spring, the body condition of R. giurinus was significantly higher in the PH than in the LH. The body condition of R. cliffordpopei did not differ significantly between habitats in the four seasons. These findings demonstrate that the two congeneric and introduced goby species occupy distinct habitats, indicating that spatial segregation enables coexistence of the two invasive species at high abundances within an ecosystem.Spatial segregation is one of the most important mechanisms that facilitates coexistence among competing species. Large populations of two introduced and congeneric goby species (Rhinogobius giurinus and Rhinogobius cliffordpopei) now co-occur in Lake Erhai, a plateau lake in the Yunnan-Guizhou Plateau (China). Herein we quantified the spatio-temporal distribution of the two species to determine whether spatial segregation occurred within the same ecosystem. A total of 67,819 individuals of R. giurinus and 36,043 of R. cliffordpopei were sampled across four seasons. The results indicated that R. giurinus mostly occupied profundal habitat (PH) while R. cliffordpopei mainly used littoral habitat (LH). Correlation analysis revealed the abundance of R. giurinus was positively associated with deep water, silt and coarse sand substrata, whereas the distribution of R. cliffordpopei was positively associated with high densities of macrozooplanktons and high abundances of other fish species, high concentration of dissolved oxygen and high densities of submerged macrophytes. Except in spring, the body condition of R. giurinus was significantly higher in the PH than in the LH. The body condition of R. cliffordpopei did not differ significantly between habitats in the four seasons. These findings demonstrate that the two congeneric and introduced goby species occupy distinct habitats, indicating that spatial segregation enables coexistence of the two invasive species at high abundances within an ecosystem