Genomic insights into high exopolysaccharideproducing dairy starter bacterium Streptococcus thermophilus ASCC 1275

Conference Theme: Linking animal science and animal agriculture: Meeting the global demands of 2050Graduate Student Competition: ADSA Dairy Foods OralStreptococcus thermophilus ASCC 1275 (ST 1275) is a typical dairy starter bacterium and produces the highest known amount (1,000 mg/L) of exopolysaccharide (EPS) in milk within this species. This organism produces both capsular and ropy EPS and possesses textural modifying properties for yogurt and cheese. In this study, de novo shotgun paired-end pyrosequencing was applied to complete the whole genome of ST 1275. The genome size of ST 1275, a plasmid-free bacterium, was 1.85 Mbp with an average GC content of 39.1%. A novel eps gene cluster for EPS assembly containing two-pair genes of epsC- epsD for determining the chain length of EPS was found in ST 1275 genome, which confirms that ST 1275 produces two types of EPSs as found in our previous studies. Compared with other sequenced S. thermophilus strains, ST 1275 possessed the lowest numbers of 5 rRNA operons and 55 tRNAs suggesting that this organism may have a more effective protein synthesis machinery. The highest number of four separate CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) loci was found in ST 1275 genome indicating that this organism may have a better adaptive immunity against various bacteriophage infections. Further analysis including carbohydrate utilization, effective proteolytic system, sophisticated stress response systems and defense systems in ST 1275 was performed to provide genomic insights into its adaptation to milk and as a cell factory for EPS production during milk fermentation. The elucidation of ST 1275 genome makes this organism as a model dairy starter bacterium for the research of high EPS yield and capsular/ropy EPS producer from the species of S. thermophilus.published_or_final_versio

Genomic insights into high exopolysaccharide-producing dairy starter bacterium Streptococcus thermophilus ASCC 1275.

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Common distribution of gad operon in Lactobacillus brevis and its GadA contributes to efficient GABA synthesis toward cytosolic near-neutral pH

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Circulating genotypes of porcine respiratory and reproductive syndrome viruses in southern China: re-emerging lineage 3 and genomic recombination with vaccine variants

Poster presentation: PRRS Epidemiology, Heterogeneity, and EvolutionPorcine reproductive and respiratory syndrome virus (PRRSV) was first reported in China since the end of 1995 and several variants were further reported in subsequence years, causing huge economic losses to Chinese swine industry. In 2006, a country-wide outbreak of porcine high fever syndrome, caused by a highly pathogenic PRRSV (HP-PRRSV) emerged in China affecting more than 20 million pigs. To date, three lineages (lineage 3, lineage 5.1 and lineage 8.7) of PRRSV were reported in China based on our global genotyping for type 2 PRRSV. Among these three lineages, only lineage 8.7 was the most significant variant where infected pigs showing severe clinical symptoms. Much investigation to this economically important lineage (lineage 8.7) caused lesser attention on other lineages in China during recent years. Based on our viral isolation in Guangdong Province of Southern China during 2009 and 2011, the majority of isolates collected were grouped as HP-PRRSV cluster. Moreover, circulating vaccine-associated lineage (lineage 5.1) and re-emerging lineage 3 isolates were also found. Lineage 3 was previously reported in China, Hong Kong and Taiwan, but there were no reports for this lineage after 2005 in China. Here, we present the re-emerging of this lineage 3 viruses in southern China in 2010 and their evolutionary story. Additionally, we had identified inter-lineage genomic recombination between MLV vaccine strain and re-emerging lineage 3 virus in a farm practicing MLV vaccination. Although modified live virus (MLV) vaccines provide solid protection against PRRSV infection, the safety of MLV vaccines has been questioned since the detection of vaccine revertants which caused productive problems similar to those of wild-type PRRSV. Based on our experimental study, no differences in virulence between the recombinant variant and wild-type lineage 3 were observed. However, further investigations on genomic recombination among PRRSV variants in China are needed.published_or_final_versio

Towards a metagenomic understanding on enhanced biomethane production from waste activated sludge after pH 10 pretreatment

BACKGROUND: Understanding the effects of pretreatment on anaerobic digestion of sludge waste from wastewater treatment plants is becoming increasingly important, as impetus moves towards the utilization of sludge for renewable energy production. Although the field of sludge pretreatment has progressed significantly over the past decade, critical questions concerning the underlying microbial interactions remain unanswered. In this study, a metagenomic approach was adopted to investigate the microbial composition and gene content contributing to enhanced biogas production from sludge subjected to a novel pretreatment method (maintaining pH at 10 for 8 days) compared to other documented methods (ultrasonic, thermal and thermal-alkaline). RESULTS: Our results showed that pretreated sludge attained a maximum methane yield approximately 4-fold higher than that of the blank un-pretreated sludge set-up at day 17. Both the microbial and metabolic consortium shifted extensively towards enhanced biodegradation subsequent to pretreatment, providing insight for the enhanced methane yield. The prevalence of Methanosaeta thermophila and Methanothermobacter thermautotrophicus, together with the functional affiliation of enzymes-encoding genes suggested an acetoclastic and hydrogenotrophic methanogenesis pathway. Additionally, an alternative enzymology in Methanosaeta was observed. CONCLUSIONS: This study is the first to provide a microbiological understanding of improved biogas production subsequent to a novel waste sludge pretreatment method. The knowledge garnered will assist the design of more efficient pretreatment methods for biogas production in the future.published_or_final_versio

Effects of a simulation-based workshop on nursing students' competence in arterial puncture

Objective: To evaluate whether a short simulation-based workshop in radial artery puncture would improve nursing students’ competence to a level in which they could practise the procedure on a live patient without compromising his safety. Methods: Quasi-experimental one-group pretest-posttest study with 111 third-year nursing students. A 1.5-hour simulation-based workshop was implemented. This included a video-lecture, live demonstrations, selfdirected simulated practice in dyads and individual intermittent feedback. Participants’ skills, knowledge and self-efficacy in arterial puncture were measured before and after attending the workshop. Results: After the intervention, a total of 61.1% of the participants showed the level of competence required to safely practice radial artery puncture on a live patient under supervision. Conclusion: Effective simulation-based training in arterial puncture for nursing students does not necessarily need to be resource-intensive. Well-planned, evidence-based training sessions using low-tech simulators could help educators to achieve good educational outcomes and promote patient safety

Australia's Dengue Risk Driven by Human Adaptation to Climate Change

Current and projected rainfall reduction in southeast Australia has seen the installation of large numbers of government-subsidised and ad hoc domestic water storage containers that could create the possibility of the mosquito Ae. aegypti expanding out of Queensland into southern Australian's urban regions. By assessing the past and current distribution of Ae. aegypti in Australia, we construct distributional models for this dengue vector for our current climate and projected climates for 2030 and 2050. The resulting mosquito distribution maps are compared to published theoretical temperature limits for Ae. aegypti and some differences are identified. Nonetheless, synthesising our mosquito distribution maps with dengue transmission climate limits derived from historical dengue epidemics in Australia suggests that the current proliferation of domestic water storage tanks could easily result in another range expansion of Ae. aegypti along with the associated dengue risk were the virus to be introduced

Efficacy of a Non-Hypercalcemic Vitamin-D2 Derived Anti-Cancer Agent (MT19c) and Inhibition of Fatty Acid Synthesis in an Ovarian Cancer Xenograft Model

BACKGROUND:Numerous vitamin-D analogs exhibited poor response rates, high systemic toxicities and hypercalcemia in human trials to treat cancer. We identified the first non-hypercalcemic anti-cancer vitamin D analog MT19c by altering the A-ring of ergocalciferol. This study describes the therapeutic efficacy and mechanism of action of MT19c in both in vitro and in vivo models. METHODOLOGY/PRINCIPAL FINDING:Antitumor efficacy of MT19c was evaluated in ovarian cancer cell (SKOV-3) xenografts in nude mice and a syngenic rat ovarian cancer model. Serum calcium levels of MT19c or calcitriol treated animals were measured. In-silico molecular docking simulation and a cell based VDR reporter assay revealed MT19c-VDR interaction. Genomewide mRNA analysis of MT19c treated tumors identified drug targets which were verified by immunoblotting and microscopy. Quantification of cellular malonyl CoA was carried out by HPLC-MS. A binding study with PPAR-Y receptor was performed. MT19c reduced ovarian cancer growth in xenograft and syngeneic animal models without causing hypercalcemia or acute toxicity. MT19c is a weak vitamin-D receptor (VDR) antagonist that disrupted the interaction between VDR and coactivator SRC2-3. Genome-wide mRNA analysis and western blot and microscopy of MT19c treated xenograft tumors showed inhibition of fatty acid synthase (FASN) activity. MT19c reduced cellular levels of malonyl CoA in SKOV-3 cells and inhibited EGFR/phosphoinositol-3kinase (PI-3K) activity independently of PPAR-gamma protein. SIGNIFICANCE:Antitumor effects of non-hypercalcemic agent MT19c provide a new approach to the design of vitamin-D based anticancer molecules and a rationale for developing MT19c as a therapeutic agent for malignant ovarian tumors by targeting oncogenic de novo lipogenesis

Detection and Alignment of 3D Domain Swapping Proteins Using Angle-Distance Image-Based Secondary Structural Matching Techniques

This work presents a novel detection method for three-dimensional domain swapping (DS), a mechanism for forming protein quaternary structures that can be visualized as if monomers had “opened” their “closed” structures and exchanged the opened portion to form intertwined oligomers. Since the first report of DS in the mid 1990s, an increasing number of identified cases has led to the postulation that DS might occur in a protein with an unconstrained terminus under appropriate conditions. DS may play important roles in the molecular evolution and functional regulation of proteins and the formation of depositions in Alzheimer's and prion diseases. Moreover, it is promising for designing auto-assembling biomaterials. Despite the increasing interest in DS, related bioinformatics methods are rarely available. Owing to a dramatic conformational difference between the monomeric/closed and oligomeric/open forms, conventional structural comparison methods are inadequate for detecting DS. Hence, there is also a lack of comprehensive datasets for studying DS. Based on angle-distance (A-D) image transformations of secondary structural elements (SSEs), specific patterns within A-D images can be recognized and classified for structural similarities. In this work, a matching algorithm to extract corresponding SSE pairs from A-D images and a novel DS score have been designed and demonstrated to be applicable to the detection of DS relationships. The Matthews correlation coefficient (MCC) and sensitivity of the proposed DS-detecting method were higher than 0.81 even when the sequence identities of the proteins examined were lower than 10%. On average, the alignment percentage and root-mean-square distance (RMSD) computed by the proposed method were 90% and 1.8Å for a set of 1,211 DS-related pairs of proteins. The performances of structural alignments remain high and stable for DS-related homologs with less than 10% sequence identities. In addition, the quality of its hinge loop determination is comparable to that of manual inspection. This method has been implemented as a web-based tool, which requires two protein structures as the input and then the type and/or existence of DS relationships between the input structures are determined according to the A-D image-based structural alignments and the DS score. The proposed method is expected to trigger large-scale studies of this interesting structural phenomenon and facilitate related applications