Discovery and Functional Study of a Novel Genomic Locus Homologous to Bα-Mating-Type Sublocus of Lentinula edodes

The interaction of mating pheromone and pheromone receptor from the B mating-type locus is the first step in the activation of the mushroom mating signal transduction pathway. The B mating-type locus of Lentinula edodes is composed of Bα and Bβ subloci, each of which contains genes for mating pheromone and pheromone receptor. Allelic variations in both subloci generate multiple B mating-types through which L. edodes maintains genetic diversity. In addition to the B mating-type locus, our genomic sequence analysis revealed the presence of a novel chromosomal locus 43.3 kb away from the B mating-type locus, containing genes for a pair of mating pheromones (PHBN1 and PHBN2) and a pheromone receptor (RCBN). The new locus (Bα-N) was homologous to the Bα sublocus, but unlike the multiallelic Bα sublocus, it was highly conserved across the wild and cultivated strains. The interactions of RcbN with various mating pheromones from the B and Bα-N mating-type loci were investigated using yeast model that replaced endogenous yeast mating pheromone receptor STE2 with RCBN. The yeast mating signal transduction pathway was only activated in the presence of PHBN1 or PHBN2 in the RcbN producing yeast, indicating that RcbN interacts with self-pheromones (PHBN1 and PHBN2), not with pheromones from the B mating-type locus. The biological function of the Bα-N locus was suggested to control the expression of A mating-type genes, as evidenced by the increased expression of two A-genes HD1 and HD2 upon the treatment of synthetic PHBN1 and PHBN2 peptides to the monokaryotic strain of L. edodes.     

Scatter-Gather-Merge: An efficient star-join query processing algorithm for data-parallel frameworks

A data-parallel framework is very attractive for large-scale data processing since it enables such an application to easily process a huge amount of data on commodity machines. MapReduce, a popular data-parallel framework, is used in various fields such as web search, data mining and data warehouses; it is proven to be very practical for such a data-parallel application. A star-join query is a popular query in data warehouses that are a current target domain of data-parallel frameworks. This article proposes a new algorithm that efficiently processes star-join queries in data-parallel frameworks such as MapReduce and Dryad. Our star-join algorithm for general data-parallel frameworks is called Scatter-Gather-Merge, and it processes star-join queries in a constant number of computation steps, although the number of participating dimension tables increases. By adopting bloom filters, Scatter-Gather-Merge reduces a non-trivial amount of IO. We also show that Scatter-Gather-Merge can be easily applied to MapReduce. Our experimental results in both cluster and cloud environments show that Scatter-Gather-Merge outperforms existing approaches.     

Peptide rescue of an N-terminal truncation of the Stoffel fragment of taq DNA polymerase.

Deletion of the first 289 amino acids of the DNA polymerase from Thermus aquaticus (Taq polymerase) removes the 5' to 3' exonuclease domain to yield the thermostable Stoffel polymerase fragment (Lawyer et al., 1989). Preliminary N-terminal truncation studies of the Stoffel fragment suggested that removal of an additional 12 amino acids (the Stof delta 12 mutant) had no significant effect on activity or stability, but that the further truncation of the protein (the Stof delta 47, in which 47 amino acids were deleted), resulted in a significant loss of both activity and thermostability. A 33-amino acid synthetic peptide, based on this critical region (i.e., residues 303-335 inclusive), was able to restore 85% of the Stof delta 12 activity when added back to the truncated Stof delta 47 protein as well as return the temperature optimum to that of the Stof delta 12 and Stoffel proteins. Examination of the crystal structure of Taq polymerase (Kim et al., 1995) shows that residues 302-336 of the enzyme form a three-stranded beta-sheet structure that interacts with the remainder of the protein. CD analysis of the 33-amino acid peptide indicates that the free peptide also adopts an ordered structure in solution with more than 50% beta-sheet content. These data suggest that this 33-amino acid peptide constitutes a stable beta-sheet structure capable of rescuing the truncated polymerase in a fashion analogous to the well-documented complementation of Ribonuclease S protein by the 15-residue, alpha-helical, S peptide.     

Models of Individual Dietary Behavior Based on Smartphone Data: The Influence of Routine,Physical Activity,Emotion, and Food Environment

IntroductionSmartphone applications (apps) facilitate the collection of data on multiple aspects of behavior that are useful for characterizing baseline patterns and for monitoring progress in interventions aimed at promoting healthier lifestyles. Individual-based models can be used to examine whether behavior, such as diet, corresponds to certain typological patterns. The objectives of this paper are to demonstrate individual-based modeling methods relevant to a person’s eating behavior, and the value of such approach compared to typical regression models.MethodUsing a mobile app, 2 weeks of physical activity and ecological momentary assessment (EMA) data, and 6 days of diet data were collected from 12 university students recruited from a university in Kunming, a rapidly developing city in southwest China. Phone GPS data were collected for the entire 2-week period, from which exposure to various food environments along each subject’s activity space was determined. Physical activity was measured using phone accelerometry. Mobile phone EMA was used to assess self-reported emotion/feelings. The portion size of meals and food groups was determined from voice-annotated videos of meals. Individual-based regression models were used to characterize subjects as following one of 4 diet typologies: those with a routine portion sizes determined by time of day, those with portion sizes that balance physical activity (energy balance), those with portion sizes influenced by emotion, and those with portion sizes associated with food environments.ResultsAmple compliance with the phone-based behavioral assessment was observed for all participants. Across all individuals, 868 consumed food items were recorded, with fruits, grains and dairy foods dominating the portion sizes. On average, 218 hours of accelerometry and 35 EMA responses were recorded for each participant. For some subjects, the routine model was able to explain up to 47% of the variation in portion sizes, and the energy balance model was able to explain over 88% of the variation in portion sizes. Across all our subjects, the food environment was an important predictor of eating patterns. Generally, grouping all subjects into a pooled model performed worse than modeling each individual separately.ConclusionA typological modeling approach was useful in understanding individual dietary behaviors in our cohort. This approach may be applicable to the study of other human behaviors, particularly those that collect repeated measures on individuals, and those involving smartphone-based behavioral measurement.     

Diversity and community structure of ectomycorrhizal mycorrhizal fungi in roots and rhizosphere soil of Abies koreana and Taxus cuspidata in Mt. Halla

In this study, the roots and rhizosphere soil of Abies koreana and Taxus cuspidata were collected from sites at two different altitudes on Mt. Halla. Ectomycorrhizal fungi (EMF) were identified by Illumina MiSeq sequencing. The proportion of EMF from the roots was 89% in A. koreana and 69% in T. cuspidata. Among EMF in rhizosphere soils, the genus Russula was the most abundant in roots of A. koreana (p < 0.05). The altitude did not affect the biodiversity of EMF communities but influenced fungal community composition. However, the host plants had the most significant effect on EMF communities. The result of the EMF community analysis showed that even if the EMF were isolated from the same altitudes, the EMF communities differed according to the host plant. The community similarity index of EMF in the roots of A. koreana was higher than that of T. cuspidata (p < 0.05). The results show that both altitude and host plants influenced the structure of EMF communities. Conifers inhabiting harsh sub-alpine environments rely strongly on symbiotic relationships with EMF. A. koreana is an endangered species with a higher host specificity of EMF and climate change vulnerability than T. cuspidata. This study provides insights into the EMF communities, which are symbionts of A. koreana, and our critical findings may be used to restore A. koreana.     

Human Infections with Liver and Minute Intestinal Flukes in Guangxi, China: Analysis by DNA Sequencing, Ultrasonography, and Immunoaffinity Chromatography

The prevalence of liver and intestinal fluke infections was determined by surveying inhabitants of Hengxuan, Fusui, and Shanglin villages which were known to be endemic for liver flukes in Guangxi, China in May 2010. A total of 718 people were examined for helminth eggs by the Kato-Katz thick smear technique, ultrasonography, immunoaffinity chromatography, and DNA sequencing. The overall egg positive rate was found to be 59.6% (28.0-70.6%) that included mixed infections with liver and intestinal flukes. Cases showing higher than 20,000 eggs per gram of feces (EPG) were detected between 1.3% and 16.2%. Ultrasonographic findings exhibited overall 28.2% (72 of 255 cases) dilatation rate of the intrahepatic bile duct. Clonorchis sinensis infection was detected serologically in 88.3% (38 of 43 cases) among C. sinensis egg positive subjects by the immunoaffinity chromatography using a specific antigen for C. sinensis. For differential diagnosis of the liver and intestinal flukes, more precise PCR and nucleotide sequencing for copro-DNA were performed for 46 egg positive cases. Mixed infections with C. sinensis and Metagonimus yokogawai were detected in 8 of 46 egg positive cases, whereas 29 specimens were positive for Haplorchis taichui. Ultrasonographic findings and immunoaffinity chromatography results showed usefulness, even in a limited way, in figuring out of the liver fluke endemicity.     

Human Neurocysticercosis Case and an Endemic Focus of Taenia solium in Lao PDR

A male patient with neurocysticercosis was identified in Montai Village, Xay District, Oudomxay Province, Lao PDR in February 2004. He had a history of diagnosis for neurocysticercosis by a CT scan in Thailand after an onset of epileptic seizure in 1993. A pig in the same district was found to contain Taenia solium metacestodes (=cysticerci); the slaughtered pig body contained more than 2,000 cysticerci. In addition to morphological identification, molecular identification was also performed on the cysticerci by DNA sequencing analysis of the mitochondrial cox1 gene; they were confirmed as T. solium metacestodes. The patient is regarded as an indigenous case of neurocysticercosis infected in an endemic focus of T. solium taeniasis/cysticercosis in Oudomxay Province, Lao PDR.