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  • 1
    Online Resource
    Online Resource
    A Draft Sequence of the Rice Genome ( Oryza sativa L. ssp. indica )
    American Association for the Advancement of Science (AAAS) ; 2002
    In:  Science Vol. 296, No. 5565 ( 2002-04-05), p. 79-92
    Details
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 296, No. 5565 ( 2002-04-05), p. 79-92
    Abstract: We have produced a draft sequence of the rice genome for the most widely cultivated subspecies in China, Oryza sativa L. ssp. indica , by whole-genome shotgun sequencing. The genome was 466 megabases in size, with an estimated 46,022 to 55,615 genes. Functional coverage in the assembled sequences was 92.0%. About 42.2% of the genome was in exact 20-nucleotide oligomer repeats, and most of the transposons were in the intergenic regions between genes. Although 80.6% of predicted Arabidopsis thaliana genes had a homolog in rice, only 49.4% of predicted rice genes had a homolog in A. thaliana . The large proportion of rice genes with no recognizable homologs is due to a gradient in the GC content of rice coding sequences.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    URL: Article
    DOI: 10.1126/science.1068037
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2002
    detail.hit.zdb_id: 128410-1
    detail.hit.zdb_id: 2066996-3
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  • 2
    Online Resource
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    A single transcription factor promotes both yield and immunity in rice
    American Association for the Advancement of Science (AAAS) ; 2018
    In:  Science Vol. 361, No. 6406 ( 2018-09-07), p. 1026-1028
    Details
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 361, No. 6406 ( 2018-09-07), p. 1026-1028
    Abstract: Plant immunity often penalizes growth and yield. The transcription factor Ideal Plant Architecture 1 (IPA1) reduces unproductive tillers and increases grains per panicle, which results in improved rice yield. Here we report that higher IPA1 levels enhance immunity. Mechanistically, phosphorylation of IPA1 at amino acid Ser 163 within its DNA binding domain occurs in response to infection by the fungus Magnaporthe oryzae and alters the DNA binding specificity of IPA1. Phosphorylated IPA1 binds to the promoter of the pathogen defense gene WRKY45 and activates its expression, leading to enhanced disease resistance. IPA1 returns to a nonphosphorylated state within 48 hours after infection, resuming support of the growth needed for high yield. Thus, IPA1 promotes both yield and disease resistance by sustaining a balance between growth and immunity.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    URL: Article
    DOI: 10.1126/science.aat7675
    RVK:
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2018
    detail.hit.zdb_id: 128410-1
    detail.hit.zdb_id: 2066996-3
    detail.hit.zdb_id: 2060783-0
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  • 3
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    Transcriptome-wide subtyping of pediatric and adult T cell acute lymphoblastic leukemia in an international study of 707 cases
    Proceedings of the National Academy of Sciences ; 2022
    In:  Proceedings of the National Academy of Sciences Vol. 119, No. 15 ( 2022-04-12)
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 119, No. 15 ( 2022-04-12)
    Abstract: T cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy of T cell progenitors, known to be a heterogeneous disease in pediatric and adult patients. Here we attempted to better understand the disease at the molecular level based on the transcriptomic landscape of 707 T-ALL patients (510 pediatric, 190 adult patients, and 7 with unknown age; 599 from published cohorts and 108 newly investigated). Leveraging the information of gene expression enabled us to identify 10 subtypes (G1–G10), including the previously undescribed one characterized by GATA3 mutations, with GATA3 R276Q capable of affecting lymphocyte development in zebrafish. Through associating with T cell differentiation stages, we found that high expression of LYL1/LMO2/SPI1/HOXA (G1–G6) might represent the early T cell progenitor, pro/precortical/cortical stage with a relatively high age of disease onset, and lymphoblasts with TLX3/TLX1 high expression (G7–G8) could be blocked at the cortical/postcortical stage, while those with high expression of NKX2-1/TAL1/LMO1 (G9–G10) might correspond to cortical/postcortical/mature stages of T cell development. Notably, adult patients harbored more cooperative mutations among epigenetic regulators, and genes involved in JAK-STAT and RAS signaling pathways, with 44% of patients aged 40 y or above in G1 bearing DNMT3A/IDH2 mutations usually seen in acute myeloid leukemia, suggesting the nature of mixed phenotype acute leukemia.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.2120787119
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2022
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  • 4
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    Loss of function of a rice TPR-domain RNA-binding protein confers broad-spectrum disease resistance
    Proceedings of the National Academy of Sciences ; 2018
    In:  Proceedings of the National Academy of Sciences Vol. 115, No. 12 ( 2018-03-20), p. 3174-3179
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 115, No. 12 ( 2018-03-20), p. 3174-3179
    Abstract: Crops carrying broad-spectrum resistance loci provide an effective strategy for controlling infectious disease because these loci typically confer resistance to diverse races of a pathogen or even multiple species of pathogens. Despite their importance, only a few crop broad-spectrum resistance loci have been reported. Here, we report the identification and characterization of the rice bsr-k1 (broad-spectrum resistance Kitaake-1) mutant, which confers broad-spectrum resistance against Magnaporthe oryzae and Xanthomonas oryzae pv oryzae with no major penalty on key agronomic traits. Map-based cloning reveals that Bsr-k1 encodes a tetratricopeptide repeats (TPRs)-containing protein, which binds to mRNAs of multiple OsPAL ( OsPAL1–7 ) genes and promotes their turnover. Loss of function of the Bsr-k1 gene leads to accumulation of OsPAL1–7 mRNAs in the bsr-k1 mutant. Furthermore, overexpression of OsPAL1 in wild-type rice TP309 confers resistance to M. oryzae , supporting the role of OsPAL1 . Our discovery of the bsr-k1 allele constitutes a significant conceptual advancement and provides a valuable tool for breeding broad-spectrum resistant rice.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.1705927115
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2018
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
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  • 5
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    Rapid diversification of five Oryza AA genomes associated with rice adaptation
    Proceedings of the National Academy of Sciences ; 2014
    In:  Proceedings of the National Academy of Sciences Vol. 111, No. 46 ( 2014-11-18)
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 111, No. 46 ( 2014-11-18)
    Abstract: Comparative genomic analyses among closely related species can greatly enhance our understanding of plant gene and genome evolution. We report de novo-assembled AA-genome sequences for Oryza nivara , Oryza glaberrima , Oryza barthii , Oryza glumaepatula , and Oryza meridionalis . Our analyses reveal massive levels of genomic structural variation, including segmental duplication and rapid gene family turnover, with particularly high instability in defense-related genes. We show, on a genomic scale, how lineage-specific expansion or contraction of gene families has led to their morphological and reproductive diversification, thus enlightening the evolutionary process of speciation and adaptation. Despite strong purifying selective pressures on most Oryza genes, we documented a large number of positively selected genes, especially those genes involved in flower development, reproduction, and resistance-related processes. These diversifying genes are expected to have played key roles in adaptations to their ecological niches in Asia, South America, Africa and Australia. Extensive variation in noncoding RNA gene numbers, function enrichment, and rates of sequence divergence might also help account for the different genetic adaptations of these rice species. Collectively, these resources provide new opportunities for evolutionary genomics, numerous insights into recent speciation, a valuable database of functional variation for crop improvement, and tools for efficient conservation of wild rice germplasm.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.1418307111
    RVK:
    TA 1000
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    WA 15000
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2014
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
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  • 6
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    Haplotype-specific MAPK3 expression in 16p11.2 deletion contributes to variable neurodevelopment
    Oxford University Press (OUP) ; 2023
    In:  Brain Vol. 146, No. 8 ( 2023-08-01), p. 3347-3363
    Details
    In: Brain, Oxford University Press (OUP), Vol. 146, No. 8 ( 2023-08-01), p. 3347-3363
    Abstract: Recurrent proximal 16p11.2 deletion (16p11.2del) is a risk factor for diverse neurodevelopmental disorders with incomplete penetrance and variable expressivity. Although investigation with human induced pluripotent stem cell models has confirmed disruption of neuronal development in 16p11.2del neuronal cells, which genes are responsible for abnormal cellular phenotypes and what determines the penetrance of neurodevelopmental abnormalities are unknown. We performed haplotype phasing of the 16p11.2 region in a 16p11.2del neurodevelopmental disorders cohort and generated human induced pluripotent stem cells for two 16p11.2del families with distinct residual haplotypes and variable neurodevelopmental disorder phenotypes. Using transcriptomic profiles and cellular phenotypes of the human induced pluripotent stem cell-differentiated cortex neuronal cells, we revealed MAPK3 to be a contributor to dysfunction in multiple pathways related to early neuronal development, with altered soma and electrophysiological properties in mature neuronal cells. Notably, MAPK3 expression in 16p11.2del neuronal cells varied on the basis of a 132 kb 58 single nucleotide polymorphism (SNP) residual haplotype, with the version composed entirely of minor alleles associated with reduced MAPK3 expression. Ten SNPs on the residual haplotype were mapped to enhancers of MAPK3. We functionally validated six of these SNPs by luciferase assay, implicating them in the residual haplotype-specific differences in MAPK3 expression via cis-regulation. Finally, the analysis of three different cohorts of 16p11.2del subjects showed that this minor residual haplotype is associated with neurodevelopmental disorder phenotypes in 16p11.2del carriers.
    Type of Medium: Online Resource
    ISSN: 0006-8950 , 1460-2156
    URL: Article
    DOI: 10.1093/brain/awad071
    RVK:
    XA 10000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 1474117-9
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  • 7
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    Attention Modulates the Role of Speakers' Voice Identity and Linguistic Information in Spoken Word Processing: Evidence From Event-Related Potentials
    American Speech Language Hearing Association ; 2023
    In:  Journal of Speech, Language, and Hearing Research Vol. 66, No. 5 ( 2023-05-09), p. 1678-1693
    Details
    In: Journal of Speech, Language, and Hearing Research, American Speech Language Hearing Association, Vol. 66, No. 5 ( 2023-05-09), p. 1678-1693
    Abstract: The human voice usually contains two types of information: linguistic and identity information. However, whether and how linguistic information interacts with identity information remains controversial. This study aimed to explore the processing of identity and linguistic information during spoken word processing by considering the modulation of attention. Method: We conducted two event-related potentials (ERPs) experiments in the study. Different speakers (self, friend, and unfamiliar speakers) and emotional words (positive, negative, and neutral words) were used to manipulate the identity and linguistic information. With the manipulation, Experiment 1 explored the identity and linguistic information processing with a word decision task that requires participants' explicit attention to linguistic information. Experiment 2 further investigated the issue with a passive oddball paradigm that requires rare attention to either the identity or linguistic information. Results: Experiment 1 revealed an interaction among speaker, word type, and hemisphere in N400 amplitudes but not in N100 and P200, which suggests that identity information interacted with linguistic information at the later stage of spoken word processing. The mismatch negativity results of Experiment 2 showed no significant interaction between speaker and word pair, which indicates that identity and linguistic information were processed independently. Conclusions: The identity information would interact with linguistic information during spoken word processing. However, the interaction was modulated by the task demands on attention involvement. We propose an attention-modulated explanation to explain the mechanism underlying identity and linguistic information processing. Implications of our findings are discussed in light of the integration and independence theories.
    Type of Medium: Online Resource
    ISSN: 1092-4388 , 1558-9102
    URL: Article
    DOI: 10.1044/2023_JSLHR-22-00420
    Language: English
    Publisher: American Speech Language Hearing Association
    Publication Date: 2023
    detail.hit.zdb_id: 2070420-3
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  • 8
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    Targeting presynaptic H3 heteroreceptor in nucleus accumbens to improve anxiety and obsessive-compulsive-like behaviors
    Proceedings of the National Academy of Sciences ; 2020
    In:  Proceedings of the National Academy of Sciences Vol. 117, No. 50 ( 2020-12-15), p. 32155-32164
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 117, No. 50 ( 2020-12-15), p. 32155-32164
    Abstract: Anxiety commonly co‐occurs with obsessive-compulsive disorder (OCD). Both of them are closely related to stress. However, the shared neurobiological substrates and therapeutic targets remain unclear. Here we report an amelioration of both anxiety and OCD via the histamine presynaptic H3 heteroreceptor on glutamatergic afferent terminals from the prelimbic prefrontal cortex (PrL) to the nucleus accumbens (NAc) core, a vital node in the limbic loop. The NAc core receives direct hypothalamic histaminergic projections, and optogenetic activation of hypothalamic NAc core histaminergic afferents selectively suppresses glutamatergic rather than GABAergic synaptic transmission in the NAc core via the H3 receptor and thus produces an anxiolytic effect and improves anxiety- and obsessive-compulsive-like behaviors induced by restraint stress. Although the H3 receptor is expressed in glutamatergic afferent terminals from the PrL, basolateral amygdala (BLA), and ventral hippocampus (vHipp), rather than the thalamus, only the PrL– and not BLA– and vHipp–NAc core glutamatergic pathways among the glutamatergic afferent inputs to the NAc core is responsible for co-occurrence of anxiety- and obsessive-compulsive-like behaviors. Furthermore, activation of the H3 receptor ameliorates anxiety and obsessive-compulsive-like behaviors induced by optogenetic excitation of the PrL–NAc glutamatergic afferents. These results demonstrate a common mechanism regulating anxiety- and obsessive-compulsive-like behaviors and provide insight into the clinical treatment strategy for OCD with comorbid anxiety by targeting the histamine H3 receptor in the NAc core.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.2008456117
    RVK:
    TA 1000
    RVK:
    WA 15000
    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2020
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
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  • 9
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    Effects of native language experience on Mandarin lexical tone processing in proficient second language learners
    Wiley ; 2019
    In:  Psychophysiology Vol. 56, No. 11 ( 2019-11)
    Details
    In: Psychophysiology, Wiley, Vol. 56, No. 11 ( 2019-11)
    Abstract: Both the acoustic and phonological information in L2 lexical tones is important to L2 lexical tone learning. The present study uses behavioral and neurophysiological measures to examine L2 learners’ processing of acoustic and phonological information, and reveals the differences between L2 learners with tonal native languages versus those with nontonal native languages on the processing of these two types of information. It sheds insights into the understanding of L2 lexical tone learning and offers a testable approach for future studies on L2 speech acquisition.
    Type of Medium: Online Resource
    ISSN: 0048-5772 , 1469-8986
    URL: Issue
    URL: Article
    DOI: 10.1111/psyp.v56.11
    DOI: 10.1111/psyp.13448
    RVK:
    CL 1000
    Language: English
    Publisher: Wiley
    Publication Date: 2019
    detail.hit.zdb_id: 1484299-3
    SSG: 5,2
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  • 10
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    How Different Types of Linguistic Information Impact Voice Perception: Evidence From the Language-Familiarity Effect
    SAGE Publications ; 2023
    In:  Language and Speech
    Details
    In: Language and Speech, SAGE Publications
    Abstract: Previous studies have suggested the effect of linguistic information on voice perception (e.g., the language-familiarity effect [LFE]). However, it remains unclear which type of specific information in speech contributes to voice perception, including acoustic, phonological, lexical, and semantic information. It is also underexamined whether the roles of these different types of information are modulated by the experimental paradigm (speaker discrimination vs. speaker identification). In this study, we conducted two experiments to investigate these issues regarding LFEs. Experiment 1 examined the roles of acoustic and phonological information in speaker discrimination and identification with forward and time-reversed Mandarin and Indonesian sentences. Experiment 2 further identified the roles of phonological, lexical, and semantic information with forward, word-scrambled, and reconstructed (consisting of pseudo-Mandarin words) Mandarin and forward Indonesian sentences. For Mandarin-only participants, in Experiment 1, speaker discrimination was more accurate for forward than reversed sentences, but there was no LFE in either sentence. Speaker identification was also more accurate for forward than reversed sentences, whereas there was an LFE for forward sentences. In Experiment 2, speaker discrimination was better for word-scrambled than reconstructed Mandarin sentences. Speaker identification was more accurate for forward and word-scrambled Mandarin sentences but less accurate for Mandarin reconstructed and forward Indonesian sentences. In general, the pattern of the results for Indonesian learners was the same as that for Mandarin-only speakers. These results suggest that different kinds of information support speaker discrimination and identification in native and unfamiliar languages. The LFE in speaker identification depends on both phonological and lexical information.
    Type of Medium: Online Resource
    ISSN: 0023-8309 , 1756-6053
    URL: Article
    DOI: 10.1177/00238309221143062
    RVK:
    EQ 1000
    Language: English
    Publisher: SAGE Publications
    Publication Date: 2023
    detail.hit.zdb_id: 2001596-3
    SSG: 5,2
    SSG: 7,11
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