Sophia Zhang - Academia.edu (original) (raw)

Papers by Sophia Zhang

Microscopy research and technique, 2015

Telenomus dendrolimusi Chu is a dominant egg parasitoid of Dendrolimus, which is the most serious... more Telenomus dendrolimusi Chu is a dominant egg parasitoid of Dendrolimus, which is the most serious conifer defoliator in China. However, the host locating mechanism of T. dendrolimusi is unclear. To take better advantage of this kind of parasitoid, it is necessary to clarify the basic knowledge of the organization of the wasp's sensory system. In this study, the external morphologies of the sensilla on the entire female and male T. dendrolimusi body were described using scanning electron microscopy. Antennae shape and sensilla types were sexually dimorphic. Ten segments and nine types of sensilla were found on the female antenna, including basiconic sensillum (BS), chaeticum sensillum (ChS), trichoid sensillum type 1 (TS1), trichoid sensillum type 2 (TS2), trichoid curvata sensillum (TCS), sickle-shaped sensillum (SSS), multiporous gustatory sensillum (MGS), campaniform sensillum (CS), and styloconica sensillum (STS). The distribution of the sensilla was directional on female ant...

Aging

We have shown before that constitutive DNA damage signaling represented by H2AX-Ser139 phosphoryl... more We have shown before that constitutive DNA damage signaling represented by H2AX-Ser139 phosphorylation and ATM activation in untreated normal and tumor cells is a reporter of the persistent DNA replication stress induced by endogenous oxidants, the by-products of aerobic respiration. In the present study we observed that exposure of normal mitogenically stimulated lymphocytes or tumor cell lines A549, TK6 and A431 to metformin, the specific activator of 5'AMP-activated protein kinase (AMPK) and an inhibitor of mTOR signaling, resulted in attenuation of constitutive H2AX phosphorylation and ATM activation. The effects were metformin-concentration dependent and seen even at the pharmacologically pertinent 0.1 mM drug concentration. The data also show that intracellular levels of endogenous reactive oxidants able to oxidize 2',7'-dihydro-dichlorofluorescein diacetate was reduced in metformin-treated cells. Since persistent constitutive DNA replication stress, particularly w...

Aging, 2011

We have shown before that constitutive DNA damage signaling represented by H2AX-Ser139 phosphoryl... more We have shown before that constitutive DNA damage signaling represented by H2AX-Ser139 phosphorylation and ATM activation in untreated normal and tumor cells is a reporter of the persistent DNA replication stress induced by endogenous oxidants, the by-products of aerobic respiration. In the present study we observed that exposure of normal mitogenically stimulated lymphocytes or tumor cell lines A549, TK6 and A431 to metformin, the specific activator of 5'AMP-activated protein kinase (AMPK) and an inhibitor of mTOR signaling, resulted in attenuation of constitutive H2AX phosphorylation and ATM activation. The effects were metformin-concentration dependent and seen even at the pharmacologically pertinent 0.1 mM drug concentration. The data also show that intracellular levels of endogenous reactive oxidants able to oxidize 2',7'-dihydro-dichlorofluorescein diacetate was reduced in metformin-treated cells. Since persistent constitutive DNA replication stress, particularly w...

Insect biochemistry and molecular biology, 2014

The Yunnan pine and Simao pine caterpillar moths, Dendrolimus houi Lajonquière and Dendrolimus ki... more The Yunnan pine and Simao pine caterpillar moths, Dendrolimus houi Lajonquière and Dendrolimus kikuchii Matsumura (Lepidoptera: Lasiocampidae), are two closely related and sympatric pests of coniferous forests in southwestern China, and olfactory communication systems of these two insects have received considerable attention because of their economic importance. However, there is little information on the molecular aspect of odor detection about these insects. Furthermore, although lepidopteran species have been widely used in studies of insect olfaction, few work made comparison between sister moths on the olfactory recognition mechanisms. In this study, next-generation sequencing of the antennal transcriptome of these two moths were performed to identify the major olfactory genes. After comparing the antennal transcriptome of these two moths, we found that they exhibit highly similar transcripts-associated GO terms. Chemosensory gene families were further analyzed in both species....

Microscopy research and technique, 2013

Insects rely heavily on olfaction to locate habitat, mates, and oviposition sites, while odorant ... more Insects rely heavily on olfaction to locate habitat, mates, and oviposition sites, while odorant molecules and the antennal olfactory sensory cells of insects are two indispensable components of olfactory response. Our previous work identified the sex pheromones and volatile compounds derived from host plant of Dendrolimus tabulaeformis Tsai et Liu, a serious economic pest of pines in northern China. However, little is known about the olfactory system of D. tabulaeformis, especially in females. To make a better understanding of the D. tabulaeformis olfactory response, we investigated the structure, innervation, numbers, and distribution of sensilla on the antennae of male and female moth, based on scanning and transmission electron microscopy. The pinniform antennae of this moth bear five types of sensilla: trichoid (TS), basiconica (BS), styloconic (StS), and chaetica (ChS) sensilla, and belt-type structures (BTSs). The BTSs are hollow and are not chemical sensilla. The ChSs occur ...

Cell Cycle, 2014

We recently reported that the p12 subunit of human DNA polymerase δ (Pol δ4) is degraded by CRL4(... more We recently reported that the p12 subunit of human DNA polymerase δ (Pol δ4) is degraded by CRL4(Cdt2) which regulates the licensing factor Cdt1 and p21(WAF1) during the G1 to S transition. Presently, we performed multiparameter laser scanning cytometric analyses of changes in levels of p12, Cdt1 and p21(WAF1), detected immunocytochemically in individual cells, vis-à-vis the initiation and completion of DNA replication. The latter was assessed by pulse-labeling A549 cells with the DNA precursor ethynyl-2'-deoxyribose (EdU). The loss of p12 preceded the initiation of DNA replication and essentially all cells incorporating EdU were p12 negative. Completion of DNA replication and transition to G2 phase coincided with the re-appearance and rapid rise of p12 levels. Similar to p12 a decline of p21(WAF1) and Cdt1 was seen at the end of G1 phase and all DNA replicating cells were p21(WAF1) and Cdt1 negative. The loss of p21(WAF1) preceded that of Cdt1 and p12 and the disappearance of the latter coincided with the onset of DNA replication. Loss of p12 leads to conversion of Pol δ4 to its trimeric form, Pol δ3, so that the results provide strong support to the notion that Pol δ3 is engaged in DNA replication during unperturbed progression through the S phase of cell cycle. Also assessed was a correlation between EdU incorporation, likely reflecting the rate of DNA replication in individual cells, and the level of expression of positive biomarkers of replication cyclin A, PCNA and Ki-67 in these cells. Of interest was the observation of stronger correlation between EdU incorporation and expression of PCNA (r = 0.73) than expression of cyclin A (r = 0.47) or Ki-67 (r = 0.47).

Microscopy Research and Technique, 2012

In this article, we described the ultrastructure of the sensilla on the antenna, eyes, mouthparts... more In this article, we described the ultrastructure of the sensilla on the antenna, eyes, mouthparts, wings, legs, and external genitalia of female and male Trichogramma dendrolimi using scanning electron microscopy (SEM). The antenna possessed the most sensilla types. We found 13 types of sensilla on female antenna, which were trichoid sensilla (TS) type 1-4, chaetica sensilla (ChS) type 1-2, campaniform sensilla (CaS), falcate sensilla, placoid sensilla (PS) type 1-2, basiconic capitate peg sensilla (BCPS) type 1, coeloconic sensilla (CoS), and styloconic sensilla. Ten types of sensilla were found on the male antenna, some were the same as that on female T. dendrolimi antenna, such as TS types 1 and 3, CaS, PS type 1, BCPS type 1, and CoS, but TS types 5 and 6, ChS type 3, and BCPS 2 were specific to male T. dendrolimi antenna. The leg possesses eight types of sensilla and a kind of tympana structure. Four types of TSs were found on the wings. On the mouthparts, sensilla on the maxillary and labial palps were unique, including two TSs and one ChS. The ovipositor possesses three types of sensilla, and the copulatory organ possesses two types. The eyes had only one kind of TS. Furthermore, external morphology of antenna and external genitalia revealed distinct sexual dimorphisms. According to their morphology, the possible functions of these sensilla were discussed. These results may further our understanding of the sensory mechanisms of T. dendrolimi in response to infochemicals within the environment. Microsc. Res. Tech. 75:1513-1521, 2012

Yeast, 2012

Red yeasts hold great promise in the production of microbial lipids and carotenoids. Genetic stud... more Red yeasts hold great promise in the production of microbial lipids and carotenoids. Genetic study of red yeasts has attracted much attention; however, rapid amplification of genes from red yeast samples remains technically challenging. Here a highly efficient method for the preparation of genomic DNA (gDNA) template, which could be directly used for PCR, was developed. Cells from colonies or liquid cultures were collected and sequentially treated by microwave, plMAN5C, proteinase K and boiling (MMPB) in a single tube to give cell lysates that were qualified as PCR templates. Single-copied gDNA fragments o up to 2.8 kb were successfully amplified. We also demonstrated successful application of this method for species in the Ascomycetes and Basidiomycetes and identification of two leucine auxotroph mutants of Rhodotorula glutinis. This method could be widely employed for the screening and genetic engineering of various yeasts. sents the results of the MMPB method; each lane 2 negative control; each lane 3 gDNA amplification results; and each lane M, 250 bp DNA ladder marker 472 X. Lin et al.

PloS one, 2010

In a tritrophic system formed by a plant, an herbivore and a natural enemy, each component has it... more In a tritrophic system formed by a plant, an herbivore and a natural enemy, each component has its own biological rhythm. However, the rhythm correlations among the three levels and the underlying mechanisms in any tritrophic system are largely unknown. Here, we report that the rhythms exhibited bidirectional correlations in a model tritrophic system involving a lima bean, a pea leafminer and a parasitoid. From the bottom-up perspective, the rhythm was initiated from herbivore feeding, which triggered the rhythms of volatile emissions; then the rhythmic pattern of parasitoid activities was affected, and these rhythms were synchronized by a light switch signal. Increased volatile concentration can enhance the intensity of parasitoid locomotion and oviposition only under light. From the top-down perspective, naive and oviposition-experienced parasitoids were able to utilize the different volatile rhythm information from the damaged plant to locate host leafminers respectively. Our res...

World Journal of Microbiology and Biotechnology, 2011

Here we report an improved method for targeted gene disruption with high efficiency in S. cerevis... more Here we report an improved method for targeted gene disruption with high efficiency in S. cerevisiae, where the selection markers with long homologous arms are defined by the choice of the primer binding sites at the target locus and the disruption cassettes are constructed by restriction-free (RF) cloning strategy. Three genes, SAM1, IDH1 and IDH2, were disrupted with this method and the disruption efficiencies of SAM1 was improved several folds with much lower false-positive rates compared to the conventional one-step PCR-based gene disruption method. This approach for gene disruption cassettes construction with long flanking homologous arms may be readily applicable to facilitate targeted gene disruption in other non-conventional yeasts and fungi.

Process Biochemistry, 2012

Inulinase is an important enzyme used in the high fructose syrup and other related industries. A ... more Inulinase is an important enzyme used in the high fructose syrup and other related industries. A more cost-effective approach is required for producing highly active inulinase. In this study, the gene encoding inulinase of the yeast Kluyveromyces marxianus CBS 6556 was expressed in methylotrophic host Pichia pastoris and secretory production of recombinant inulinase (rKmINU) in the yeast under methanol induction was achieved. The purified rKmINU showed a specific activity of 2714 U/mg, which is over 12-fold higher than those of other inulinases described previously. It displayed excellent stability from 30 to 50 • C and pH 3.0-5.0, and the half-life of rKmINU was over 96 h under these conditions. Moreover, rKmINU saccharified Jerusalem artichoke tuber juice effectively.

PLoS ONE, 2007

Background. Plant volatiles play an important role in defending plants against insect attacks by ... more Background. Plant volatiles play an important role in defending plants against insect attacks by attracting their natural enemies. For example, green leaf volatiles (GLVs) and terpenoids emitted from herbivore-damaged plants were found to be important in the host location of parasitic wasps. However, evidence of the functional roles and mechanisms of these semiochemicals from a system of multiple plants in prey location by the parasitoid is limited. Little is known about the potential evolutionary trends between herbivore-induced host plant volatiles and the host location of their parasitoids. Methodology/ Principal Findings. The present study includes hierarchical cluster analyses of plant volatile profiles from seven families of host and non-host plants of pea leafminer, Liriomyza huidobrensis, and behavioral responses of a naive parasitic wasp, Opius dissitus, to some principal volatile compounds. Here we show that plants can effectively pull wasps, O. dissitus, towards them by releasing a universally induced compound, (Z)-3-hexenol, and potentially keep these plants safe from parasitic assaults by leafminer pests, L. huidobrensis. Specifically, we found that volatile profiles from healthy plants revealed a partly phylogenetic signal, while the inducible compounds of the infested-plants did not result from the fact that the induced plant volatiles dominate most of the volatile blends of the host and non-host plants of the leafminer pests. We further show that the parasitoids are capable of distinguishing the damaged host plant from the non-host plant of the leafminers. Conclusions/ Significance. Our results suggest that, as the most passive scenario of plant involvement, leafminers and mechanical damages evoke similar semio-chemicals. Using ubiquitous compounds, such as hexenol, for host location by general parasitoids could be an adaptation of the most conservative evolution of tritrophic interaction. Although for this, other compounds may be used to improve the precision of the host location by the parasitoids.

PLoS ONE, 2011

Eukaryotic DNA polymerase d (pol d) plays a crucial role in chromosomal DNA replication and vario... more Eukaryotic DNA polymerase d (pol d) plays a crucial role in chromosomal DNA replication and various DNA repair processes. It is thought to consist of p125, p66 (p68), p50 and p12 subunits. However, rigorous isolation of mammalian pol d from natural sources has usually yielded two-subunit preparations containing only p125 and p50 polypeptides. While recombinant pol d isolated from infected insect cells have some problems of consistency in the quality of the preparations, and the yields are much lower. To address these deficiencies, we have constructed recombinant BmNPV baculoviruses using MultiBac system. This method makes the generation of recombinant forms of pol d containing mutations in any one of the subunits or combinations thereof extremely facile. From about 350 infected larvae, we obtained as much as 4 mg of pol d four-subunit complex. Highly purified enzyme behaved like the one of native form by rigorous characterization and comparison of its activities on poly(dA)/oligo(dT) template-primer and singly primed M13 DNA, and its homogeneity on FPLC gel filtration. In vitro base excision repair (BER) assays showed that pol d plays a significant role in uracil-intiated BER and is more likely to mediate LP BER, while the trimer lacking p12 is more likely to mediate SN BER. It seems likely that loss of p12 modulates the rate of SN BER and LP BER during the repair process. Thus, this work provides a simple, fast, reliable and economic way for the large-scale production of human DNA polymerase d with a high activity and purity, setting up a new platform for our further research on the biochemical properties of pol d, its regulation and the integration of its functions, and how alterations in pol d function could contribute to the etiology of human cancer or other diseases that can result from loss of genomic stability.

PLoS ONE, 2012

Background: Exposure of plants to herbivore-induced plant volatiles (HIPVs) alters their resistan... more Background: Exposure of plants to herbivore-induced plant volatiles (HIPVs) alters their resistance to herbivores. However, the whole-genome transcriptional responses of treated plants remain unknown, and the signal pathways that produce HIPVs are also unclear.

PLoS ONE, 2011

Mammalian DNA polymerase d (pol d), a four-subunit enzyme, plays a crucial and versatile role in ... more Mammalian DNA polymerase d (pol d), a four-subunit enzyme, plays a crucial and versatile role in DNA replication and various DNA repair processes. Its function as a chromosomal DNA polymerase is dependent on the association with proliferating cell nuclear antigen (PCNA) which functions as a molecular sliding clamp. All four of the pol d subunits (p125, p50, p68, and p12) have been reported to bind to PCNA. However, the identity of the subunit of pol d that directly interacts with PCNA and is therefore primarily responsible for the processivity of the enzyme still remains controversial. Previous model for the network of protein-protein interactions of the pol d-PCNA complex showed that pol d might be able to interact with a single molecule of PCNA homotrimer through its three subunits, p125, p68, and p12 in which the p50 was not included in. Here, we have confirmed that the small subunit p50 of human pol d truthfully interacts with PCNA by the use of far-Western analysis, quantitative ELISA assay, and subcellular co-localization. P50 is required for mediation of the interaction between pol d subassemblies and PCNA homotrimer. Thus, pol d interacts with PCNA via its four subunits.

Plant Signaling & Behavior, 2013

Rhythms of volatiles release from healthy and insect-damaged Phaseolus vulgaris. Plant Signal Beh... more Rhythms of volatiles release from healthy and insect-damaged Phaseolus vulgaris. Plant Signal Behav 2013; 8:e25759; http://dx.doi.org/1 0.4161/psb.25759

Nucleic Acids Research, 2008

Human DNA polymerase delta (Pol delta4), a key enzyme in chromosomal replication, is a heterotetr... more Human DNA polymerase delta (Pol delta4), a key enzyme in chromosomal replication, is a heterotetramer composed of the p125, p50, p68 and p12 subunits. Genotoxic agents such as UV and alkylating chemicals trigger a DNA damage response in which Pol delta4 is converted to a trimer (Pol delta3) by degradation of p12. We show that Pol delta3 has altered enzymatic properties: it is less able to perform translesion synthesis on templates containing base lesions (O(6)-MeG, 8-oxoG, an abasic site or a thymine-thymine dimer); a greater proofreading activity; an increased exonuclease/polymerase activity ratio; a decreased tendency for the insertion of wrong nucleotides, and for the extension of mismatched primers. Overall, our findings indicate that Pol delta3 exhibits an enhanced ability for the detection of errors in both primers and templates over its parent enzyme. These alterations in Pol delta3 show that p12 plays a major role in Pol delta4 catalytic functions, and provides significant insights into the rationale for the conversion of Pol delta4 to Pol delta3 in the cellular response to DNA damage.

Nature Communications, 2012

Triacylglycerols are among the most attractive alternative raw materials for biofuel development.... more Triacylglycerols are among the most attractive alternative raw materials for biofuel development. Current oil plant-based technologies are limited in terms of triacylglycerol production capacity and rate. These limitations may be circumvented by biotransformation of carbohydrates into lipids; however, our understanding of microbial oleaginicity remains limited. Here we present the results of a multi-omic analysis of Rhodosporidium toruloides, a robust triacylglycerol-producing fungus. The assembly of genome and transcriptome sequencing data reveals a genome of 20.2 mb containing 8,171 protein-coding genes, the majority of which have multiple introns. Genes including a novel fatty acid synthase are predicted to participate in metabolic pathways absent in non-oleaginous yeasts. Transcriptomic and proteomic data suggest that lipid accumulation under nitrogen-limited conditions correlates with the induction of lipogenesis, nitrogenous compound recycling, macromolecule metabolism and autophagy. The multi-omic map of R. toruloides therefore provides a valuable resource for efforts to rationally engineer lipid-production pathways.

Molecular Biotechnology, 2010

The malic enzyme-encoding cDNA (GQ372891) from the oleaginous yeast Lipomyces starkeyi AS 2.1560 ... more The malic enzyme-encoding cDNA (GQ372891) from the oleaginous yeast Lipomyces starkeyi AS 2.1560 was isolated, which has an 1719-bp open reading frame flanked by a 290-bp 5 0 untranslated sequence and a 92-bp 3 0 untranslated sequence. The proposed gene, LsME1, encoded a protein with 572 amino acid residues. The protein presented 58% sequence identity with the malic enzymes from Yarrowia lipolytica CLIB122 and Aspergillus fumigatus Af293. The LsME1 gene was cloned into the vector pMAL-p4x to express a fusion protein (MBP-LsME1) in Escherichia coli TB1. The fusion protein was purified and then cleaved by Factor Xa to give the recombinant LsME1. This purified enzyme took either NAD ? or NADP ? as the coenzyme but preferred NAD ? . The K m values for malic acid, NAD ? and NADP ? were 0.85 ± 0.05 mM, 0.34 ± 0.08 mM, and 7.4 ± 0.32 mM, respectively, at pH 7.3.

Molecular Biotechnology, 2011

Oleaginous yeast Rhodosporidium toruloides is an excellent microbial lipid producer. Therefore, i... more Oleaginous yeast Rhodosporidium toruloides is an excellent microbial lipid producer. Therefore, it is important to develop molecular biology tools to understand the basic mechanism for lipid accumulation and further manipulate the microorganism. High-quality RNA extraction from R. toruloides is particularly challenging due to high level of polysaccharides, lipids, and other secondary metabolites. To obtain an optimal protocol for RNA extraction from R. toruloides, four methods were evaluated. Large difference in RNA yield and quality among these protocols was found. The optimum method was modified RNAiso procedure, where RNA was isolated using liquid nitrogen-RNAiso method with salt precipitation and the addition of β-mercaptoethanol. This method consistently recovered RNA in good quality with high yield. Around 297 μg total RNA per gram of cells was obtained with an average purity measured as A₂₆₀/A₂₈₀ of 2.09. A titer of 10⁵ cfu/ml could be harvested to construct a full-length cDNA library with the RNA sample in this quality. Electrophoresis gel analysis indicated the fragments ranged from 200 bp to 4.0 kb, with the average size of 1000 bp. Randomly picked clones showed the recombination efficiency at 80%. These results showed that RNA of R. toruloides was successfully extracted for the first time using the modified RNAiso method, and the cDNA library was appropriate for screening the genes related to lipid accumulation.

Microscopy research and technique, 2015

Telenomus dendrolimusi Chu is a dominant egg parasitoid of Dendrolimus, which is the most serious... more Telenomus dendrolimusi Chu is a dominant egg parasitoid of Dendrolimus, which is the most serious conifer defoliator in China. However, the host locating mechanism of T. dendrolimusi is unclear. To take better advantage of this kind of parasitoid, it is necessary to clarify the basic knowledge of the organization of the wasp's sensory system. In this study, the external morphologies of the sensilla on the entire female and male T. dendrolimusi body were described using scanning electron microscopy. Antennae shape and sensilla types were sexually dimorphic. Ten segments and nine types of sensilla were found on the female antenna, including basiconic sensillum (BS), chaeticum sensillum (ChS), trichoid sensillum type 1 (TS1), trichoid sensillum type 2 (TS2), trichoid curvata sensillum (TCS), sickle-shaped sensillum (SSS), multiporous gustatory sensillum (MGS), campaniform sensillum (CS), and styloconica sensillum (STS). The distribution of the sensilla was directional on female ant...

Aging

We have shown before that constitutive DNA damage signaling represented by H2AX-Ser139 phosphoryl... more We have shown before that constitutive DNA damage signaling represented by H2AX-Ser139 phosphorylation and ATM activation in untreated normal and tumor cells is a reporter of the persistent DNA replication stress induced by endogenous oxidants, the by-products of aerobic respiration. In the present study we observed that exposure of normal mitogenically stimulated lymphocytes or tumor cell lines A549, TK6 and A431 to metformin, the specific activator of 5'AMP-activated protein kinase (AMPK) and an inhibitor of mTOR signaling, resulted in attenuation of constitutive H2AX phosphorylation and ATM activation. The effects were metformin-concentration dependent and seen even at the pharmacologically pertinent 0.1 mM drug concentration. The data also show that intracellular levels of endogenous reactive oxidants able to oxidize 2',7'-dihydro-dichlorofluorescein diacetate was reduced in metformin-treated cells. Since persistent constitutive DNA replication stress, particularly w...

Aging, 2011

We have shown before that constitutive DNA damage signaling represented by H2AX-Ser139 phosphoryl... more We have shown before that constitutive DNA damage signaling represented by H2AX-Ser139 phosphorylation and ATM activation in untreated normal and tumor cells is a reporter of the persistent DNA replication stress induced by endogenous oxidants, the by-products of aerobic respiration. In the present study we observed that exposure of normal mitogenically stimulated lymphocytes or tumor cell lines A549, TK6 and A431 to metformin, the specific activator of 5'AMP-activated protein kinase (AMPK) and an inhibitor of mTOR signaling, resulted in attenuation of constitutive H2AX phosphorylation and ATM activation. The effects were metformin-concentration dependent and seen even at the pharmacologically pertinent 0.1 mM drug concentration. The data also show that intracellular levels of endogenous reactive oxidants able to oxidize 2',7'-dihydro-dichlorofluorescein diacetate was reduced in metformin-treated cells. Since persistent constitutive DNA replication stress, particularly w...

Insect biochemistry and molecular biology, 2014

The Yunnan pine and Simao pine caterpillar moths, Dendrolimus houi Lajonquière and Dendrolimus ki... more The Yunnan pine and Simao pine caterpillar moths, Dendrolimus houi Lajonquière and Dendrolimus kikuchii Matsumura (Lepidoptera: Lasiocampidae), are two closely related and sympatric pests of coniferous forests in southwestern China, and olfactory communication systems of these two insects have received considerable attention because of their economic importance. However, there is little information on the molecular aspect of odor detection about these insects. Furthermore, although lepidopteran species have been widely used in studies of insect olfaction, few work made comparison between sister moths on the olfactory recognition mechanisms. In this study, next-generation sequencing of the antennal transcriptome of these two moths were performed to identify the major olfactory genes. After comparing the antennal transcriptome of these two moths, we found that they exhibit highly similar transcripts-associated GO terms. Chemosensory gene families were further analyzed in both species....

Microscopy research and technique, 2013

Insects rely heavily on olfaction to locate habitat, mates, and oviposition sites, while odorant ... more Insects rely heavily on olfaction to locate habitat, mates, and oviposition sites, while odorant molecules and the antennal olfactory sensory cells of insects are two indispensable components of olfactory response. Our previous work identified the sex pheromones and volatile compounds derived from host plant of Dendrolimus tabulaeformis Tsai et Liu, a serious economic pest of pines in northern China. However, little is known about the olfactory system of D. tabulaeformis, especially in females. To make a better understanding of the D. tabulaeformis olfactory response, we investigated the structure, innervation, numbers, and distribution of sensilla on the antennae of male and female moth, based on scanning and transmission electron microscopy. The pinniform antennae of this moth bear five types of sensilla: trichoid (TS), basiconica (BS), styloconic (StS), and chaetica (ChS) sensilla, and belt-type structures (BTSs). The BTSs are hollow and are not chemical sensilla. The ChSs occur ...

Cell Cycle, 2014

We recently reported that the p12 subunit of human DNA polymerase δ (Pol δ4) is degraded by CRL4(... more We recently reported that the p12 subunit of human DNA polymerase δ (Pol δ4) is degraded by CRL4(Cdt2) which regulates the licensing factor Cdt1 and p21(WAF1) during the G1 to S transition. Presently, we performed multiparameter laser scanning cytometric analyses of changes in levels of p12, Cdt1 and p21(WAF1), detected immunocytochemically in individual cells, vis-à-vis the initiation and completion of DNA replication. The latter was assessed by pulse-labeling A549 cells with the DNA precursor ethynyl-2'-deoxyribose (EdU). The loss of p12 preceded the initiation of DNA replication and essentially all cells incorporating EdU were p12 negative. Completion of DNA replication and transition to G2 phase coincided with the re-appearance and rapid rise of p12 levels. Similar to p12 a decline of p21(WAF1) and Cdt1 was seen at the end of G1 phase and all DNA replicating cells were p21(WAF1) and Cdt1 negative. The loss of p21(WAF1) preceded that of Cdt1 and p12 and the disappearance of the latter coincided with the onset of DNA replication. Loss of p12 leads to conversion of Pol δ4 to its trimeric form, Pol δ3, so that the results provide strong support to the notion that Pol δ3 is engaged in DNA replication during unperturbed progression through the S phase of cell cycle. Also assessed was a correlation between EdU incorporation, likely reflecting the rate of DNA replication in individual cells, and the level of expression of positive biomarkers of replication cyclin A, PCNA and Ki-67 in these cells. Of interest was the observation of stronger correlation between EdU incorporation and expression of PCNA (r = 0.73) than expression of cyclin A (r = 0.47) or Ki-67 (r = 0.47).

Microscopy Research and Technique, 2012

In this article, we described the ultrastructure of the sensilla on the antenna, eyes, mouthparts... more In this article, we described the ultrastructure of the sensilla on the antenna, eyes, mouthparts, wings, legs, and external genitalia of female and male Trichogramma dendrolimi using scanning electron microscopy (SEM). The antenna possessed the most sensilla types. We found 13 types of sensilla on female antenna, which were trichoid sensilla (TS) type 1-4, chaetica sensilla (ChS) type 1-2, campaniform sensilla (CaS), falcate sensilla, placoid sensilla (PS) type 1-2, basiconic capitate peg sensilla (BCPS) type 1, coeloconic sensilla (CoS), and styloconic sensilla. Ten types of sensilla were found on the male antenna, some were the same as that on female T. dendrolimi antenna, such as TS types 1 and 3, CaS, PS type 1, BCPS type 1, and CoS, but TS types 5 and 6, ChS type 3, and BCPS 2 were specific to male T. dendrolimi antenna. The leg possesses eight types of sensilla and a kind of tympana structure. Four types of TSs were found on the wings. On the mouthparts, sensilla on the maxillary and labial palps were unique, including two TSs and one ChS. The ovipositor possesses three types of sensilla, and the copulatory organ possesses two types. The eyes had only one kind of TS. Furthermore, external morphology of antenna and external genitalia revealed distinct sexual dimorphisms. According to their morphology, the possible functions of these sensilla were discussed. These results may further our understanding of the sensory mechanisms of T. dendrolimi in response to infochemicals within the environment. Microsc. Res. Tech. 75:1513-1521, 2012

Yeast, 2012

Red yeasts hold great promise in the production of microbial lipids and carotenoids. Genetic stud... more Red yeasts hold great promise in the production of microbial lipids and carotenoids. Genetic study of red yeasts has attracted much attention; however, rapid amplification of genes from red yeast samples remains technically challenging. Here a highly efficient method for the preparation of genomic DNA (gDNA) template, which could be directly used for PCR, was developed. Cells from colonies or liquid cultures were collected and sequentially treated by microwave, plMAN5C, proteinase K and boiling (MMPB) in a single tube to give cell lysates that were qualified as PCR templates. Single-copied gDNA fragments o up to 2.8 kb were successfully amplified. We also demonstrated successful application of this method for species in the Ascomycetes and Basidiomycetes and identification of two leucine auxotroph mutants of Rhodotorula glutinis. This method could be widely employed for the screening and genetic engineering of various yeasts. sents the results of the MMPB method; each lane 2 negative control; each lane 3 gDNA amplification results; and each lane M, 250 bp DNA ladder marker 472 X. Lin et al.

PloS one, 2010

In a tritrophic system formed by a plant, an herbivore and a natural enemy, each component has it... more In a tritrophic system formed by a plant, an herbivore and a natural enemy, each component has its own biological rhythm. However, the rhythm correlations among the three levels and the underlying mechanisms in any tritrophic system are largely unknown. Here, we report that the rhythms exhibited bidirectional correlations in a model tritrophic system involving a lima bean, a pea leafminer and a parasitoid. From the bottom-up perspective, the rhythm was initiated from herbivore feeding, which triggered the rhythms of volatile emissions; then the rhythmic pattern of parasitoid activities was affected, and these rhythms were synchronized by a light switch signal. Increased volatile concentration can enhance the intensity of parasitoid locomotion and oviposition only under light. From the top-down perspective, naive and oviposition-experienced parasitoids were able to utilize the different volatile rhythm information from the damaged plant to locate host leafminers respectively. Our res...

World Journal of Microbiology and Biotechnology, 2011

Here we report an improved method for targeted gene disruption with high efficiency in S. cerevis... more Here we report an improved method for targeted gene disruption with high efficiency in S. cerevisiae, where the selection markers with long homologous arms are defined by the choice of the primer binding sites at the target locus and the disruption cassettes are constructed by restriction-free (RF) cloning strategy. Three genes, SAM1, IDH1 and IDH2, were disrupted with this method and the disruption efficiencies of SAM1 was improved several folds with much lower false-positive rates compared to the conventional one-step PCR-based gene disruption method. This approach for gene disruption cassettes construction with long flanking homologous arms may be readily applicable to facilitate targeted gene disruption in other non-conventional yeasts and fungi.

Process Biochemistry, 2012

Inulinase is an important enzyme used in the high fructose syrup and other related industries. A ... more Inulinase is an important enzyme used in the high fructose syrup and other related industries. A more cost-effective approach is required for producing highly active inulinase. In this study, the gene encoding inulinase of the yeast Kluyveromyces marxianus CBS 6556 was expressed in methylotrophic host Pichia pastoris and secretory production of recombinant inulinase (rKmINU) in the yeast under methanol induction was achieved. The purified rKmINU showed a specific activity of 2714 U/mg, which is over 12-fold higher than those of other inulinases described previously. It displayed excellent stability from 30 to 50 • C and pH 3.0-5.0, and the half-life of rKmINU was over 96 h under these conditions. Moreover, rKmINU saccharified Jerusalem artichoke tuber juice effectively.

PLoS ONE, 2007

Background. Plant volatiles play an important role in defending plants against insect attacks by ... more Background. Plant volatiles play an important role in defending plants against insect attacks by attracting their natural enemies. For example, green leaf volatiles (GLVs) and terpenoids emitted from herbivore-damaged plants were found to be important in the host location of parasitic wasps. However, evidence of the functional roles and mechanisms of these semiochemicals from a system of multiple plants in prey location by the parasitoid is limited. Little is known about the potential evolutionary trends between herbivore-induced host plant volatiles and the host location of their parasitoids. Methodology/ Principal Findings. The present study includes hierarchical cluster analyses of plant volatile profiles from seven families of host and non-host plants of pea leafminer, Liriomyza huidobrensis, and behavioral responses of a naive parasitic wasp, Opius dissitus, to some principal volatile compounds. Here we show that plants can effectively pull wasps, O. dissitus, towards them by releasing a universally induced compound, (Z)-3-hexenol, and potentially keep these plants safe from parasitic assaults by leafminer pests, L. huidobrensis. Specifically, we found that volatile profiles from healthy plants revealed a partly phylogenetic signal, while the inducible compounds of the infested-plants did not result from the fact that the induced plant volatiles dominate most of the volatile blends of the host and non-host plants of the leafminer pests. We further show that the parasitoids are capable of distinguishing the damaged host plant from the non-host plant of the leafminers. Conclusions/ Significance. Our results suggest that, as the most passive scenario of plant involvement, leafminers and mechanical damages evoke similar semio-chemicals. Using ubiquitous compounds, such as hexenol, for host location by general parasitoids could be an adaptation of the most conservative evolution of tritrophic interaction. Although for this, other compounds may be used to improve the precision of the host location by the parasitoids.

PLoS ONE, 2011

Eukaryotic DNA polymerase d (pol d) plays a crucial role in chromosomal DNA replication and vario... more Eukaryotic DNA polymerase d (pol d) plays a crucial role in chromosomal DNA replication and various DNA repair processes. It is thought to consist of p125, p66 (p68), p50 and p12 subunits. However, rigorous isolation of mammalian pol d from natural sources has usually yielded two-subunit preparations containing only p125 and p50 polypeptides. While recombinant pol d isolated from infected insect cells have some problems of consistency in the quality of the preparations, and the yields are much lower. To address these deficiencies, we have constructed recombinant BmNPV baculoviruses using MultiBac system. This method makes the generation of recombinant forms of pol d containing mutations in any one of the subunits or combinations thereof extremely facile. From about 350 infected larvae, we obtained as much as 4 mg of pol d four-subunit complex. Highly purified enzyme behaved like the one of native form by rigorous characterization and comparison of its activities on poly(dA)/oligo(dT) template-primer and singly primed M13 DNA, and its homogeneity on FPLC gel filtration. In vitro base excision repair (BER) assays showed that pol d plays a significant role in uracil-intiated BER and is more likely to mediate LP BER, while the trimer lacking p12 is more likely to mediate SN BER. It seems likely that loss of p12 modulates the rate of SN BER and LP BER during the repair process. Thus, this work provides a simple, fast, reliable and economic way for the large-scale production of human DNA polymerase d with a high activity and purity, setting up a new platform for our further research on the biochemical properties of pol d, its regulation and the integration of its functions, and how alterations in pol d function could contribute to the etiology of human cancer or other diseases that can result from loss of genomic stability.

PLoS ONE, 2012

Background: Exposure of plants to herbivore-induced plant volatiles (HIPVs) alters their resistan... more Background: Exposure of plants to herbivore-induced plant volatiles (HIPVs) alters their resistance to herbivores. However, the whole-genome transcriptional responses of treated plants remain unknown, and the signal pathways that produce HIPVs are also unclear.

PLoS ONE, 2011

Mammalian DNA polymerase d (pol d), a four-subunit enzyme, plays a crucial and versatile role in ... more Mammalian DNA polymerase d (pol d), a four-subunit enzyme, plays a crucial and versatile role in DNA replication and various DNA repair processes. Its function as a chromosomal DNA polymerase is dependent on the association with proliferating cell nuclear antigen (PCNA) which functions as a molecular sliding clamp. All four of the pol d subunits (p125, p50, p68, and p12) have been reported to bind to PCNA. However, the identity of the subunit of pol d that directly interacts with PCNA and is therefore primarily responsible for the processivity of the enzyme still remains controversial. Previous model for the network of protein-protein interactions of the pol d-PCNA complex showed that pol d might be able to interact with a single molecule of PCNA homotrimer through its three subunits, p125, p68, and p12 in which the p50 was not included in. Here, we have confirmed that the small subunit p50 of human pol d truthfully interacts with PCNA by the use of far-Western analysis, quantitative ELISA assay, and subcellular co-localization. P50 is required for mediation of the interaction between pol d subassemblies and PCNA homotrimer. Thus, pol d interacts with PCNA via its four subunits.

Plant Signaling & Behavior, 2013

Rhythms of volatiles release from healthy and insect-damaged Phaseolus vulgaris. Plant Signal Beh... more Rhythms of volatiles release from healthy and insect-damaged Phaseolus vulgaris. Plant Signal Behav 2013; 8:e25759; http://dx.doi.org/1 0.4161/psb.25759

Nucleic Acids Research, 2008

Human DNA polymerase delta (Pol delta4), a key enzyme in chromosomal replication, is a heterotetr... more Human DNA polymerase delta (Pol delta4), a key enzyme in chromosomal replication, is a heterotetramer composed of the p125, p50, p68 and p12 subunits. Genotoxic agents such as UV and alkylating chemicals trigger a DNA damage response in which Pol delta4 is converted to a trimer (Pol delta3) by degradation of p12. We show that Pol delta3 has altered enzymatic properties: it is less able to perform translesion synthesis on templates containing base lesions (O(6)-MeG, 8-oxoG, an abasic site or a thymine-thymine dimer); a greater proofreading activity; an increased exonuclease/polymerase activity ratio; a decreased tendency for the insertion of wrong nucleotides, and for the extension of mismatched primers. Overall, our findings indicate that Pol delta3 exhibits an enhanced ability for the detection of errors in both primers and templates over its parent enzyme. These alterations in Pol delta3 show that p12 plays a major role in Pol delta4 catalytic functions, and provides significant insights into the rationale for the conversion of Pol delta4 to Pol delta3 in the cellular response to DNA damage.

Nature Communications, 2012

Triacylglycerols are among the most attractive alternative raw materials for biofuel development.... more Triacylglycerols are among the most attractive alternative raw materials for biofuel development. Current oil plant-based technologies are limited in terms of triacylglycerol production capacity and rate. These limitations may be circumvented by biotransformation of carbohydrates into lipids; however, our understanding of microbial oleaginicity remains limited. Here we present the results of a multi-omic analysis of Rhodosporidium toruloides, a robust triacylglycerol-producing fungus. The assembly of genome and transcriptome sequencing data reveals a genome of 20.2 mb containing 8,171 protein-coding genes, the majority of which have multiple introns. Genes including a novel fatty acid synthase are predicted to participate in metabolic pathways absent in non-oleaginous yeasts. Transcriptomic and proteomic data suggest that lipid accumulation under nitrogen-limited conditions correlates with the induction of lipogenesis, nitrogenous compound recycling, macromolecule metabolism and autophagy. The multi-omic map of R. toruloides therefore provides a valuable resource for efforts to rationally engineer lipid-production pathways.

Molecular Biotechnology, 2010

The malic enzyme-encoding cDNA (GQ372891) from the oleaginous yeast Lipomyces starkeyi AS 2.1560 ... more The malic enzyme-encoding cDNA (GQ372891) from the oleaginous yeast Lipomyces starkeyi AS 2.1560 was isolated, which has an 1719-bp open reading frame flanked by a 290-bp 5 0 untranslated sequence and a 92-bp 3 0 untranslated sequence. The proposed gene, LsME1, encoded a protein with 572 amino acid residues. The protein presented 58% sequence identity with the malic enzymes from Yarrowia lipolytica CLIB122 and Aspergillus fumigatus Af293. The LsME1 gene was cloned into the vector pMAL-p4x to express a fusion protein (MBP-LsME1) in Escherichia coli TB1. The fusion protein was purified and then cleaved by Factor Xa to give the recombinant LsME1. This purified enzyme took either NAD ? or NADP ? as the coenzyme but preferred NAD ? . The K m values for malic acid, NAD ? and NADP ? were 0.85 ± 0.05 mM, 0.34 ± 0.08 mM, and 7.4 ± 0.32 mM, respectively, at pH 7.3.

Molecular Biotechnology, 2011

Oleaginous yeast Rhodosporidium toruloides is an excellent microbial lipid producer. Therefore, i... more Oleaginous yeast Rhodosporidium toruloides is an excellent microbial lipid producer. Therefore, it is important to develop molecular biology tools to understand the basic mechanism for lipid accumulation and further manipulate the microorganism. High-quality RNA extraction from R. toruloides is particularly challenging due to high level of polysaccharides, lipids, and other secondary metabolites. To obtain an optimal protocol for RNA extraction from R. toruloides, four methods were evaluated. Large difference in RNA yield and quality among these protocols was found. The optimum method was modified RNAiso procedure, where RNA was isolated using liquid nitrogen-RNAiso method with salt precipitation and the addition of β-mercaptoethanol. This method consistently recovered RNA in good quality with high yield. Around 297 μg total RNA per gram of cells was obtained with an average purity measured as A₂₆₀/A₂₈₀ of 2.09. A titer of 10⁵ cfu/ml could be harvested to construct a full-length cDNA library with the RNA sample in this quality. Electrophoresis gel analysis indicated the fragments ranged from 200 bp to 4.0 kb, with the average size of 1000 bp. Randomly picked clones showed the recombination efficiency at 80%. These results showed that RNA of R. toruloides was successfully extracted for the first time using the modified RNAiso method, and the cDNA library was appropriate for screening the genes related to lipid accumulation.