Differentiation of Indica-Japonica rice revealed by insertion/deletion (InDel) fragments obtained from the comparative genomic study of DNA sequences between 93-11 ( Indica ) and Nipponbare ( Japonica )

DNA polymorphisms from nucleotide insertion/deletions (InDels) in genomic sequences are the basis for developing InDel molecular markers. To validate the InDel primer pairs on the basis of the comparative genomic study on DNA sequences between an Indica rice 93-11 and a Japonica rice Nipponbare for identifying Indica and Japonica rice varieties and studying wild Oryza species, we studied 49 Indica, 43 Japonica, and 24 wild rice accessions collected from ten Asian countries using 45 InDel primer pairs. Results indicated that of the 45 InDel primer pairs, 41 can accurately identify Indica and Japonica rice varieties with a reliability of over 80%. The scatter plotting data of the principal component analysis (PCA) indicated that: (i) the InDel primer pairs can easily distinguish Indica from Japonica rice varieties, in addition to revealing their genetic differentiation; (ii) the AA-genome wild rice species showed a relatively close genetic relationship with the Indica rice varieties; and (iii) the non-AA genome wild rice species did not show evident differentiation into the Indica and Japonica types. It is concluded from the study that most of the InDel primer pairs obtained from DNA sequences of 93-11 and Nipponbare can be used for identifying Indica and Japonica rice varieties, and for studying genetic relationships of wild rice species, particularly in terms of the Indica-Japonica differentiation. Translated from Journal of Fudan University (Natural Science), 2006, 45(3): 309–315 [译自: 复旦学报(自然科学版)]     

The Asian Lineage of Zika Virus: Transmission and Evolution in Asia and the Americas

Since first isolation in 1947 from the Zika forest in Uganda, Zika virus(ZIKV) has been principally known as a benign agent associated with sporadic human infections in a restricted number of African countries. However, during 2015–2016,an Asian lineage of ZIKV caused an unprecedentedly large outbreak in the Americas and sizeable numbers of exported cases across the globe. In this review, we critically appraise the recent advances in molecular epidemiological studies of ZIKV performed to date, and we highlight the pivotal role played by genomic surveillance in elucidating the origins,dissemination and evolution of the Asian lineage of ZIKV in Asia and in the Americas.     

Effects of Asian dust input on eukaryotic phytoplankton community structure in the open areas in the Northwestern Pacific Ocean

To study the effects of aerosol particulates originated from Asian dust on the growth of eukaryotic phytoplankton in the oligotrophic open ocean, we conducted deck-board incubation experiments in the oligotrophic region of Northwestern Pacific Ocean (NWPO). Our results showed that when dust was added at a concentration of 2?mg/L (Dust-2), the NO₃^–N concentration increased by 3.2 fold, and chlorophyll a (chl a) concentration of nano- and micro-eukaryotic phytoplankton increased, while that of pico-eukaryotic phytoplankton did not change significantly. The microphytoplankton abundance increased but the species number decreased in Dust-2. Community structure of eukaryotic microphytoplankton also changed after dust addition. The abundance of diatoms in Dust-2 (23,072 cells/L) was 4.0 fold of that in the control (5750 cells/L), and 2.4 fold of that in Dust-1 (0.2?mg/L of dust addition) (9425 cells/L) at the 7th day of incubation. Abundance of dinoflagellates decreased in Dust-2, being 42.2% that of the control at the 7th day of the incubation. Effects of dust addition on the growth of phytoplankton differed among the dominant genera: growth of Pseudo-nitzschia and Chaetoceros were promoted while that of Prorocentrum was inhibited, and growth of Thalassiosira, Heterocapsa and Scrippsiella was not influenced significantly. The growth of nano- and pico-eukaryotic phytoplankton was promoted, with the cell abundance in Dust-2 2.4 fold of that in control. Our results indicated that Asian dust-originated aerosol particulates could provide nutrients to the oligotrophic NWPO, increase the marine productivity in the area, and alter the eukaryotic phytoplankton community structure.     

Growth and protein synthesis of barramundi, Lates calcarifer, fed lupin as a partial protein replacement

Protein synthesis is an essential growth process in all animals. Little information is available on post-prandial protein synthesis and even less where different protein sources are compared. Protein synthesis was measured at 4 and 24 h after feeding juvenile barramundi in order to determine the effect of using lupin as a partial protein replacement for fish meal on the post-prandial protein metabolism. Juvenile barramundi (4.3 ±0.6 g) were held in a recirculation system (27 °C, salinity 10‰ and 24 h light) for 15 days. Fish were fed one of two isonitrogenous isoenergetic diets (40% crude protein, 16% lipid and 18.5 GE MJ kg^− 1). One diet was formulated with 100% fish meal as the protein source while the other had 45% of the protein replaced with lupin ingredients (lupin kernel meal (Lupinus angustifolius) and lupin protein concentrate). All fish were fed a ration of 6%·d^− 1 and feed intake was not significantly different between the two diets. Specific growth rate (SGR) and growth efficiency (in relation to protein (PPV) and energy (PEV)) were 6.5 ± 0.14%·d^− 1, 43.8 ± 2.72% and 38.31 ± 1.56%, respectively, and were not significantly different between the two diets. There was no significant difference in protein synthesis between the two diets at 4 and 24 h after feeding, however protein synthesis was significantly higher 4 h after feeding than at 24 h (p = 0.02). Neither growth performance nor protein metabolism was altered by replacing 45% of the protein with lupin protein and indicated this to be a suitable protein source for barramundi feeds.     

Absence of reproductive conflict during queen rearing in Apis cerana

Polyandry in honeybee queens (Apis) causes many patrilines (subfamilies) within a colony, which may lead to a potential conflict of interest among workers. This may be most apparent during queen rearing when nepotistic worker behavior could influence the genetics of future generations. Several studies have searched for such conflict in European honeybees (A. mellifera), but studies on other Apis species remain lacking. We investigated the presence of reproductive conflict in A. cerana japonica by comparing the patriline proportion of queen larvae to that of adult workers. We determined the patrilines of 272 workers and 57 queen larvae using four polymorphic microsatellite markers that were sampled from queenless colonies originally derived from four naturally mated queen-right colonies. The number of patrilines in each colony was 9, 12, 8, and 7, respectively, which is lower than that observed in continental Asia. We found no difference in patriline proportion between adult workers and queen larvae. Our data support neither genetic variance for royalty or existence of worker nepotism in A. cerana japonica.     

Can we see a cohort effect on survival of Steller sea lions (Eumetopias jubatus) at Kozlova Cape rookery (eastern Kamchatka,Russia)?

Steller sea lions ( Eumetopias jubatus ) have experienced a decline in Russia as well as the United States. The causes for the decline of the Russian population may or may not overlap the causes of the decline in Alaska. The demographics of the Russian population are not well understood and are an area of interest for scientists wishing to compare and contrast the Alaskan and Russian stocks. This study uses a unique observational system to assess survival by age at a small rookery on the Kamchatka Peninsula, Kozlova Cape. We proceeded under the hypothesis that changes in environmental conditions between years would produce noticeable differences in survival of pups born in those years. We found no evidence to support our hypothesis, but did find some differences from the Alaskan population in estimated survival for the juvenile stage class. This study also provides some of the history of Steller sea lions in Russia for context.     

Prediction of estrus cyclicity in Asian elephants (Elephas maximus) through estimation of fecal progesterone metabolite: development of an enzyme-linked immuno-sorbent assay

Asian elephants (Elephas maximus), prominent “flagship species”, are listed under the category of endangered species (EN - A2c, ver. 3.1; IUCN Red List 2009) and there is a need for their conservation. This requires understanding demographic and reproductive dynamics of the species. Monitoring reproductive status of any species is traditionally being carried out through invasive blood sampling and this is restrictive for large animals such as wild or semi-captive elephants due to legal, ethical, and practical reasons. Hence, there is a need for a non-invasive technique to assess reproductive cyclicity profiles of elephants, which will help in the species’ conservation strategies. In this study, we developed an indirect competitive enzyme linked immuno-sorbent assay (ELISA) to estimate the concentration of one of the progesterone-metabolites i.e., allopregnanolone (5α-P-3OH) in fecal samples of Asian elephants. We validated the assay which had a sensitivity of 0.25 μM at 90% binding with an EC₅₀ value of 1.37 μM. Using female elephants, kept under semi-captive conditions in the forest camps of Mudumalai Wildlife Sanctuary, Tamil Nadu and Bandipur National Park, Karnataka, India, we measured fecal progesterone-metabolite (5α-P-3OH) concentrations in six animals and showed their clear correlation with those of serum progesterone, measured by a standard radio-immuno assay. Statistical analyses using a Linear Mixed Effect model showed a positive correlation (P < 0.1) between the profiles of fecal 5α-P-3OH (range: 0.5-10 μg/g) and serum progesterone (range: 0.1-1.8 ng/mL). Therefore, our studies show, for the first time, that the fecal progesterone-metabolite assay could be exploited to predict estrus cyclicity and to potentially assess the reproductive status of captive and free-ranging female Asian elephants, thereby helping to plan their breeding strategy.     

Problems and action ideas discussed by first- and second-generation female east asian students during dream sessions.

Using Consensual Qualitative Research-Cases (CQR-C), we investigated differences in types of problems and action ideas of 7 first- and 7 second-generation female students of Asian origin as expressed in relation to working with dreams. Interpersonal issues and academic/postgraduation/career issues were typical for both groups, but first-generation Asian women more often disclosed concerns related to immigration/cultural/adjustment and distress related to physical/health issues than did second-generation Asian-American women. In terms of action ideas, both groups typically proposed interpersonal behavioral changes, but first-generation Asian women proposed changes in their thoughts and feelings more often than did second-generation Asian women. Implications for practice and research are discussed. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Development of the East Asian summer monsoon: Evidence from the sediment record in the South China Sea since 8.5 Ma

128 samples from Ocean Drilling Program (ODP) Site 1143 in the southern South China Sea were analyzed for grain size, clay minerals, biogenic opal content and quartz in order to reconstruct changes in East Asian monsoon climate since 8.5 Ma. An abrupt change of terrigenous mass accumulation rate (MAR), clay mineral assemblage, median grain size and biogenic opal MAR about 5.2 Ma suggests that between 8.5-5.2 Ma the source of terrigenous sediment was mainly in the region of surface uplift and basaltic volcanism in southern Vietnam. A simple model of East Asian summer monsoon evolution was based on the clay/feldspar ratio, kaolinite/chlorite ratio and biogenic opal MAR. The summer monsoon has two periods of maximum strength at 8.5-7.6 Ma and 7.1-6.2 Ma. Subsequently, there was a relatively stable period at 6.2-3.5 Ma, continued intensification about 3.5-2.5 Ma, and gradually weakening after 2.5 Ma. Since 1 Ma the monsoon has intensified, with remarkable high-frequency and amplitude variability. Simultaneous increase in sedimentation rates at ODP Sites 1143, 1146 and 1148, as well as in MAR of terrigenous materials, quartz, feldspar and clay minerals at ODP Site 1143 at 3.5-2.5 Ma, may be the erosional response to both global climatic deterioration and the strengthening of the East Asian summer monsoon after about 3-4 Ma.     

Mitochondrial DNA analysis in Tibet: Implications for the origin of the Tibetan population and its adaptation to high altitude

Mitochondrial DNAs (mtDNAs) of 54 Tibetans residing at altitudes ranging from 3,000–4,500 m were amplified by polymerase chain reaction (PCR), examined by high-resolution restriction endonuclease analysis, and compared with those previously described in 10 other Asian and Siberian populations. This comparison revealed that more than 50% of Asian mtDNAs belong to a unique mtDNA lineage which is found only among Mongoloids, suggesting that this lineage most likely originated in Asia at an early stage of the human colonization of that continent. Within the Tibetan mtDNAs, sets of additional linked polymorphic sites defined seven minor lineages of related mtDNA haplotypes (haplogroups). The frequency and distribution of these haplogroups in modern Asian populations are supportive of previous genetic evidence that Tibetans, although located in southern Asia, share common ancestral origins with northern Mongoloid populations. This analysis of Tibetan mtDNAs also suggests that mtDNA mutations are unlikely to play a major role in the adaptation of Tibetans to high altitudes. © 1994 Wiley-Liss, Inc.