Identification of gene-related Korean patents and construction of a database server for Korean patent sequences

With the advent of high-throughput techniques, the number of patent applications containing biological sequences has been increasing rapidly in Korea. However, there is little information on gene relatedness of the Korean patent sequences. The primary aims of this study are two-fold. First, we associated Korean patent applications with genes. Second, we have constructed a database server, named Patome@Korea, to provide the gene-patent map and the Korean patent data containing biological sequences. To associate the sequences with genes, we have received patent sequence data from the Korean Intellectual Property Office (KIPO) and annotated them with RefSeq and Entrez Gene. Through the association analysis, we found that nearly 14.7% of human genes were related to Korean patenting, compared to 25% of human genes in the US patent. We have consolidated the association results and the patent sequence data to a relational database and implemented a web-based user interface to provide search service. The database can be queried using application number, applicant, titles, gene ID/name, and RefSeq number. We also provide web-based BLAST facility to allow users to compare their sequences against patent sequences. Equal contribution.     

Polyphasic characterization of benthic cyanobacterial diversity from biofilms of the Guadarrama river (Spain): morphological,molecular, and ecological approaches1

The occurrence and environmental factors responsible for the distribution of benthic cyanobacteria in running waters remain largely unexplored in comparison with those of other aquatic ecosystems. In this study, combined data of ecological characteristics, molecular analysis (based on 16S rRNA gene), and direct microscopic inspection of environmental samples were analyzed in parallel with the morphological characterization of the isolated strains to investigate benthic cyanobacterial diversity in the Guadarrama river (Spain). A total of 17 species were identified that belonged to the genera Aphanocapsa, Pleurocapsa, Chroococcus, Chamaesiphon, Cyanobium, Pseudan‐abaena, Leptolyngbya, Phormidium, Nostoc, and Tolypothrix. Phenotypic features were associated with the results of 16S rRNA gene sequencing, complementing existing morphological and genetic databases. A decrease in the cyanobacterial diversity was observed along a pollution gradient in the river. Water quality differed among the sampling sites, and variation in nutrient content was the principal difference among locations. These characteristics were closely associated with an upstream‐downstream eutrophic gradient. Canonical correspondence analysis distinguished three groups of species with respect to the eutrophication gradient. The first group (Tolypothrix cf. tenuis, Nostoc punctiforme, Nostoc piscinale, Chamaesiphon investiens, Chroococcus minor, Leptolyngbya nostocorum, and Leptolyngbya tenuis) was characteristic of waters with low levels of nutrients. The second group (Cyanobium sp., Chamaesiphon polymorphus, Leptolyngbya boryana, Phormidium autumnale, Phormidium sp., and Aphanocapsa cf. rivularis) was characteristic of polluted waters, its members appearing mainly in great abundance under eutrophic‐hypertrophic conditions. The third group of species (Pseudanabaena catenata, Aphanocapsa muscicola, and Nostoc carneum) was present at upstream and downstream sites.     

Genetic analysis of Streptococcus agalactiae strains isolated from neonates and their mothers

Streptococcus agalactiae or group B streptococcus (GBS) is the most common cause of neonatal sepsis and meningitis in neonates. One of the major questions is whether the GBS strains able to cause neonatal invasive disease have peculiar genetic features. A collection of S. agalactiae strains, isolated from cervix, vagina and rectum of 10 mothers and from throat, ear and umbilicus of their newborns was genetically characterized by pulsed-field gel electrophoresis (PFGE). This study demonstrated that the strains isolated from each mother and her child were all genetically identical but that the strains from the 10 mother/child pairs mutually were genetically heterogeneous and 10 different PFGE patterns were found. Although it has been suggested that PFGE would be able to identify virulence traits to direct decisions in antibiotic management, the heterogeneous feature of GBS strains does not support broad application.     

Emergence of Chironomidae from Findley Lake and two ponds in the Cascade Mountains,U.S.A.

From Findley Lake and two ponds in the Cascade Mountains (U.S.A.) Chironomidae started to emerge as soon as the ice thawed in 1972 and 1973. The 1051 Chironomidae that emerged per m² from Findley Lake included 307 individuals ofTanytarsus and 358 ofProcladius. Tanytarsus outnumberedChironomus at all depths from 0 to 19.3 m. The 1506 Chironomidae that emerged per m² from the 4.5 m deep pond included 997 individuals ofTanytarsus. The 1490 Chironomidae that emerged per m² from the 2 m deep pond included 1363 Tanytarsus. The emerging biomass was 216 and 186 mg dry weight per m² in Findley Lake and the 4.5 m deep pond, respectively, and only 78 mg in the 2 m deep pond. Most species had their maximum emergence where there was organic detritus from the surrounding forest.Orthocladius emerged from sand bottom at 2.7 to 5.2 m depth.Stictochironomus emerged from mud and sand at 8.4 m depth.Chironomus emerged from soft mud at 15 to 27.5 m depth.     

Quantitative analysis of multiple forest disturbances and their compound influences on tree growth in the western U.S.

As the frequencies of extreme weather increase, forest ecosystems experience stronger influences from various disturbances. Previous research focuses on single disturbances or qualitative analysis of overlaid effects from two disturbances. Studies rarely explored the interactions between three or more disturbances, especially mechanisms behind the multiple disturbances. Our study covered four states (Idaho, Montana, Wyoming, and Utah) in the U.S. which shared similar climate patterns and vegetation distributions. We collected 241 chronologies from the International Tree-Ring Data Bank (ITRDB) and our own field expeditions. We assigned each tree ring to eight possible disturbance combinations. From the correlations between tree indices and climate (monthly temperature and total precipitation), the radial growth of tree rings showed a significant positive correlation with summer precipitation and a negative correlation with summer temperature. With three-factor ANOVA and one-way ANOVA, we ranked the impacts of each disturbance and combination of disturbances on tree growth based on tree-ring index; control (1.038) > insect (1.029) > fire (1.008) > fire & insect (0.963) > drought & insect (0.918) > drought (0.890) > drought, fire & insect (0.803) > drought & fire (0.784). We found that in most cases, the combined impact from two disturbances was larger than the impacts from single disturbances with the inclusion-exclusion principle. This research quantitatively revealed the interactions between disturbances and evaluated the effects from a combination of multiple disturbances.     

Genetic analysis of fish genomes and populations: allozyme variation within and among Atlantic salmon from Downeast rivers of Maine

Analysis of genetic variation within and among samples of naturally produced Atlantic salmon ( n  = 372) from 7 Maine (U.S.A.) and one Canadian river were conducted based on 54 allozyme loci. Eight of the 54 loci proved polymorphic, and estimated heterozygosities ( H _S) based on all loci ranged from 0·012 to 0·026 (mean = 0·021, s . e . = 0·002). Only one of 56 tests revealed genotypic proportions that deviated significantly from Hardy–Weinberg expectations. Genetic distances ( D ) between samples ranged from 0·002 to 0·022. No obvious association existed between genetic and geographic distances. Cluster analysis of genetic distances revealed the Dennys River sample as the most differentiated when all samples were included in the analysis, though bootstrap support of the cluster analysis was generally weak. G ‐tests revealed significant differences in allele frequencies among samples at five of the polymorphic loci, and the G ‐value summed over all loci also indicated significant differences among samples. F _ST values indicated that 3·4% of the total genetic diversity was due to variability among samples, while 96·6% was due to variability within samples. These results indicate that the Atlantic salmon analyzed in this study had levels of genetic variability and differentiation among samples comparable to native populations from other areas collected across a similar geographic range.     

Physical mobility under stay-at-home orders: A comparative analysis of movement restrictions between the U.S. and Europe

During the COVID-19 pandemic, both the U.S. and Europe have issued movement restrictions with the exception of visits to essential services, including groceries and pharmacies. Using Google's data on community mobility, I employ an event-study design to compare the effects of movement restrictions on physical mobility in the U.S. and Europe. I find that compared to Europe, the U.S. has higher levels of mobility related to visits to groceries and pharmacies and lower levels of the residential presence relative to baseline values, and the differences are not only statistically significant but also of large magnitudes. Such differences in post-restriction mobility are still significant between Europe and the U.S.’ early epicenters of COVID-19. The main results of this paper are robust to changes in samples and specifications. These findings suggest that movement restrictions appear to be less effective in the U.S., which have useful implications for health policy evaluation, pandemic forecasting, and economic recovery.     

基于能值分析法的矿区循环经济系统生态效率分析

从系统的角度界定了循环经济和矿区循环经济的内涵,提出了煤炭矿区循环经济系统的基本框架,并以能值分析法为基础构建了矿区循环经济系统生态效率评价指标体系与方法。运用所构建的评价指标体系与方法对山东某矿区进行了研究,得出该矿区循环经济系统2007—2011年5年间的能值效率变化趋势图和生态效率指数趋势图,研究结果与该矿区的实际发展趋势基本一致。表明运用能值分析法所建立的评价指标体系具有较强的有效性,并且对煤炭矿区发展循环经济、提高生态效率具有重要指导意义和参考价值。     

The longer you stay, the bigger you get: length of time and language use in the U.S. are associated with obesity in Puerto Rican women

This cross-sectional study examined whether length of time in the U.S., language use, and birthplace (proxy measures of acculturation) were associated with body mass index (BMI) and obesity in a sample of 174 low-income Puerto Rican women from Hartford, Connecticut. The mean BMI for the total sample (N = 174) was 27.39 (S.D. = 5.07), and nearly 34% of the sample was considered obese (BMI > or = 30). There was a statistically significant increase in BMI with length of time in the U.S. (P = 0.012) and these differences were even greater among women born in Puerto Rico (P = 0.003). Moreover, obesity prevalence was highest among women who had been in the U.S. for 10 years or more (40%), as compared to those who had been in the U.S. less than 1 year (29%; P = 0.045). There were no statistically significant associations between language and BMI for the total sample. However, among bilingual speakers born in Puerto Rico, there were significant differences in BMI according to their level of English fluency. Those who spoke fluent or very good English had a significantly higher BMI (mean = 29.72; SD = 4.12) than women whose English was good to not-so-good (mean = 26.8; SD = 5.24; P = 0.016). The findings from this study point to the need for more research on the acculturation process and obesity, in order to design culturally tailored obesity prevention programs.     

复杂疾病驱使的融合SDA-SVM集成基因挖掘方法

提出了一种新颖的复杂疾病驱使的融合SDA-SVM(Stepwise Discriminant Analysis-Support Vector Machine,SDA-SVM)技术的集成基因挖掘方法。该集成方法融合逐步判别分析和支持向量机的优点,能够有效地进行复杂疾病相关基因的深度挖掘,使得挖掘出的基因能够较好地识别疾病类型和亚型。通过将该方法应用于一套弥散性大B细胞淋巴瘤DNA表达谱数据,并与其它基因挖掘方法对比,结果表明该方法挖掘出的基因具有较高的疾病相关性和较强的疾病类型识别能力。     

REMiner: a tool for unbiased mining and analysis of repetitive elements and their arrangement structures of large chromosomes

Repetitive elements (REs) constitute a substantial portion of the genomes of human and other species; however, the RE profiles (type, density, and arrangement) within the individual genomes have not been fully characterized. In this study, we developed an RE analysis tool, called REMiner, for a chromosome-wide investigation into the occurrence of individual REs and arrangement of clusters of REs, and REMiner's functional features were examined using the human chromosome Y. The algorithm implemented by REMiner focused on unbiased mining of REs in large chromosomes and data interface within a viewer. The data from the chromosome demonstrated that REMiner is an efficient tool in regard to its capacity for a large query size and the availability of a high-resolution viewer, featuring instant retrieval of alignment data and control of magnification and identity ratio. The chromosome-wide survey identified a diverse population of ordered RE arrangements, which may participate in the genome biology.     

Dispersal distances of Tree Swallows estimated from continent-wide and limited-area data

ABSTRACT.   Dispersal is a critical link between organismal and population biology, yet, because of their mobility, our understanding of the causes and consequences of long-distance dispersal by birds remains poorly known. Methods used to study dispersal include (1) marking and recapturing individuals in a limited study area to estimate survival and dispersal rates, and (2) relying on volunteers to mark and recapture individuals over larger areas. We compared these two methods for measuring dispersal distances of Tree Swallows ( Tachycineta bicolor ) using recapture data from a limited-area study in New York State (the Swallow Dispersal Study, SDS) and the recapture dataset from the U.S. Bird Banding Laboratory (BBL). Analysis of BBL records revealed a difference in the dispersal distance distributions (DDD) for data reported before and after 1967. In the earlier data, 84% of the 238 records were for birds within 13.6 km of their first banding location, whereas only 22% of the 799 records in the more recent data were reported in this closest distance belt. These differences are almost certainly due to changes in reporting protocols instituted by the BBL in the mid-1960s. We corrected for recapture effort in the SDS, and, using this corrected SDS data for the proportion of birds returning in the closest distance belt and the recent BBL for the proportions of more distant movements, we created what we think is the best composite DDD for Tree Swallows. Even though dispersal distances up to 2367 km have been reported, the composite DDD indicates that fewer than 3% of birds disperse more than 100 km and that 85% disperse less than 15 km between years. Thus, our results suggest that the dispersal behavior of most individuals can be examined effectively at more local spatial scales. Studies of dispersal and mortality would be facilitated if all recaptures of banded birds were reported with accurate spatial coordinates to the Bird Banding Laboratory.     

The germination of mucilaginous seeds of t Plantago coronopus,Reboudia pinnata,and t Carrichtera annua on cyanobacterial soil crust from the Negev Desert

We studied the effect of intact, crushed or sterile cyanobacterial soil crust from the Negev Desert highlands of Israel as substrates for the germination of seeds of three annual plant species from local populations that produce mucilaginous seeds t Plantago coronopus, Reboudia pinnata and t Carrichtera annua. Mucilaginous seeds of these species were wetted on local intact cyanobacterial soil crust which inhibited their germination in comparison with their germination on filter paper. However, the percentage of germination of each species differed on sterile and crushed soil crust after 72 h of wetting. Germination of t Plantago coronopus seeds was inhibited mechanically and biologically on intact soil crust, since it was significantly higher on both crushed and sterile soil crust. Germination of t Reboudia pinnata seeds was slightly mechanically and biologically inhibited on intact soil crust, but germination on live crushed crust was higher than on sterile crushed crust. By contrast, germination of t Carrichtera annua seeds was not mechanically inhibited by live soil crust but there was significant biological acceleration of germination on intact soil crust relative to crushed soil crust. Each of the three species exhibited different requirements for germination. Germination of t P. coronopus is promoted by disturbances and removing the crust components (including its biological and structural effects). t R. pinnata and t C. annua germination is less affected by crust disturbance but is generally inhibited after removing the live components of the cyanobacterial crust.These species differences suggest different functions of the mucilage of the seed coat for the three species.     

Relative abundance and survival of the tick Amblyomma americanum collected from sunlit and shaded habitats

The population density of host-searching nymphal and adult lone star ticks, Amblyomma americanum (L.) (Acari: Ixodidae), was determined at the Robinson tract of the Kansas Ecological Reserves and a private farm 5 km north-west of the Robinson tract using standard drag cloth methods. Nymphs, males and females were counted and collected weekly from shaded habitats and adjacent sunlit habitats from mid-May through late July, 2003. Of the 1598 nymphs and 549 males collected by drag sampling, 74.0% and 72.1%, respectively, were collected from shaded sections of the habitats, whereas 77.3% of 472 females were found in sunlit sections. A. americanum collected during each sampling period were maintained unfed at >95% relative humidity and a 14 : 10 h photoperiod, and survival was recorded weekly until all ticks had died. Survival of nymphs, males and females did not differ between ticks collected in the shade vs. those collected in the sun. Nymphs survived significantly longer than adults, whereas male and female survival did not differ from each other. These results suggest that host-searching A. americanum populations may partition their environment to increase the chances of coming into contact with a potential vertebrate host.     

The localization of the MM isozyme of creatine phosphokinase on the surface membrane of myocardial cells and its functional coupling to ouabain-inhibited (Na+,K+)-ATPase

A rat heart plasma membrane preparation isolated in a sucrose medium and some of its enzymatic properties have been investigated.It has been shown that a rat heart plasma membrane fraction contains high creatine phosphokinase activity which can not be diminished by repeated washing with sucrose solution. Creatine phosphokinase extracted from a plasma membrane fraction with potassium chloride and 0.01% deoxycholate solution is electrophoretically identical to MM isoenzyme of creatine phosphokinase. Under the conditions where (Na⁺,K⁺)-ATPase is activated by addition of Na⁺,K⁺ and MgATP, creatine phosphokinase of plasma membrane fraction is able to maintain a low ADP concentration in the medium if creatine phosphate is present. The rate of creatine release is dependent upon MgATP concentration in accordance with the kinetic parameters of the (Na⁺,K⁺)-ATPase and is significantly inhibited by ouabain (0.5 mM). The rate of creatine release is also dependent on creatine phosphate concentration in conformance with the kinetic parameters of MM isozyme of creatine phosphokinase,It is concluded that in intact heart cells the plasma membrane creatine phosphokinase may ensure effective utilization of creatine phosphate for immediate rephosphorylation of ADP produced in the (Na⁺,K⁺)-ATPase reaction.     

X-ray-induced mutations affecting the level of the enzyme alcohol dehydrogenase in Drosophila melanogaster: frequency and genetic analysis of null-enzyme mutants.

The frequency of X-ray-induced (null-enzyme) mutations at the alcohol dehydrogenase locus in Drosophila melanogaster was measured. The rate of recovery of chromosomes that fail to direct the synthesis of a functional Adh protein is 3 x 10(-8) per R for chromosomes that do not include large chromosome rearrangements. However, this analysis excludes a larger number of chromosomes that are "null-enzyme mutations" because thye are deleted for the region of the Adh locus. The dose of X-rays required to induce a frequency of non-deletion null-enzyme mutants equal to the spontaneous frequency is about 73 rad calculated from the data reported in this communication.     

基于论文和专利的中美脑科学领域对比研究

脑科学是生命科学领域的研究前沿和热点,美国是该领域的科技强国。本文基于科技论文和专利数据,利用文献计量学的定量分析方法,比较中国和美国在脑科学领域的理论研究和应用研究的差距。结果表明,基于论文分析的理论研究对比,发现中国较美国起步晚,目前论文数量上的差距正在缩小,但学术影响力的差距较大;基于专利分析的应用研究对比,发现中国在专利申请数量上已略超过美国,但在代表专利技术价值和市场价值的国际专利数量、技术布局、龙头企业及企业参与研发比重等方面,差距还非常之大。     

H-NMR of G-U-C and G-U-C-C in D2O: assignment of nonexchangeable protons and analysis of solution conformation

The ribonucleotide oligomers G-U-C and G-U-C-C have been synthesized enzymatically. These oligomers are cognates of the m⁷G⁴⁶-U⁴⁷-C⁴⁸-m⁵C⁴⁹ sequence found in the variable loop of t-RNA^phe. The ¹H-NMR chemical shifts of the base and ribose Hl; protons as well as the couplings. J_1'–2' of the ribose protons have been examined as a function of temperature. Assignments for these resonances have been completed, and used in the analysis of solution conformation for these oligomers. The results are consistent with the basic features of the A-RNA structure and suggest the absence of alternative ordered solution structures.