Low-Toxicity and High-Efficiency Streptomyces Genome Editing Tool Based on the Miniature Type V-F CRISPR/Cas Nuclease AsCas12f1.

Genome editing tools based on SpCas9 and FnCpf1 have facilitated strain improvements for natural product production and novel drug discovery in Streptomyces. However, due to high toxicity, their editing requires high DNA transformation efficiency, which is unavailable in most streptomycetes. The transformation efficiency of an all-in-one editing tool based on miniature Cas nuclease AsCas12f1 was significantly higher than those of SpCas9 and FnCpf1 in tested streptomycetes, which is due to its small size and weak DNA cleavage activity. Using this tool, in Streptomyces coelicolor, we achieved 100% efficiency for single gene or gene cluster deletion and 46.7 and 40% efficiency for simultaneous deletion of two genes and two gene clusters, respectively. AsCas12f1 was successfully extended to Streptomyces hygroscopicus SIPI-054 for efficient genome editing, in which SpCas9/FnCpf1 does not work well. Collectively, this work offers a low-toxicity, high-efficiency genome editing tool for streptomycetes, particularly those with low DNA transformation efficiency.

Development of a CRISPR/Cas9D10A Nickase (nCas9)-Mediated Genome Editing Tool in Streptomyces.

Streptomycetes have a strong ability to produce a vast array of bioactive natural products (NPs) widely used in agriculture and veterinary/human medicine. The recently developed CRISPR/Cas9-based genome editing tools have greatly facilitated strain improvement for target NP overproduction as well as novel NP discovery in Streptomyces. However, CRISPR/Cas9 shows high toxicity to the host, limiting its application in many Streptomyces strains with a low DNA transformation efficiency. In this study, we developed a low-toxicity CRISPR/Cas9D10A nickase (nCas9)-based genome editing tool in the model strain Streptomyces coelicolor M145. We showed that in the presence of both targeting sgRNA and Cas proteins, utilization of nCas9 instead of Cas9 significantly reduced the toxicity to the host and greatly enhanced cell survival. Using this tool, we achieved deletion of single genes and gene clusters with efficiencies of 87-100 and 63-87%, and simultaneous deletion of two genes or gene clusters with efficiencies of 47 and 43%, respectively. The editing efficiency of nCas9 is comparable to that of the Cas9-mediated editing tool. Finally, the nCas9-based editing tool was successfully applied for genome editing in the industrial rapamycin-producing strain Streptomyces rapamycinicus, in which CRISPR/Cas9 cannot work well. We achieved the deletion of three tested genes with an efficiency of 27.2-30%. Collectively, the CRISPR/nCas9-based editing tool offers a convenient and efficient genetic modification system for the engineering of streptomycetes, particularly those with low DNA transformation efficiency.

The database of eye-movement measures on words in Chinese reading.

Eye movements are one of the most fundamental behaviors during reading. A growing number of Chinese reading studies have used eye-tracking techniques in the last two decades. The accumulated data provide a rich resource that can reflect the complex cognitive mechanisms underlying Chinese reading. This article reports a database of eye-movement measures of words during Chinese sentence reading. The database contains nine eye-movement measures of 8,551 Chinese words obtained from 1,718 participants across 57 Chinese sentence reading experiments. All data were collected in the same experimental environment and from homogenous participants, using the same protocols and parameters. This database enables researchers to test their theoretical or computational hypotheses concerning Chinese reading efficiently using a large number of words. The database can also indicate the processing difficulty of Chinese words during text reading, thus providing a way to control or manipulate the difficulty level of Chinese texts.

Individual differences in first-pass fixation duration in reading are related to resting-state functional connectivity.

Although there are considerable individual differences in eye movements during text reading, their neural correlates remain unclear. In this study, we investigated the relationship between the first-pass fixation duration (FPFD) in natural reading and resting-state functional connectivity (RSFC) in the brain. We defined the brain regions associated with early visual processing, word identification, attention shifts, and oculomotor control as seed regions. The results showed that individual FPFDs were positively correlated with individual RSFCs between the early visual network, visual word form area, and eye movement control/dorsal attention network. Our findings provide new evidence on the neural correlates of eye movements in text reading and indicate that individual differences in fixation time may shape the RSFC differences in the brain through the time-on-task effect and the mechanism of Hebbian learning.

Dissociating the neural correlates of the sociality and plausibility effects in simple conceptual combination.

Neuroimaging studies have indicated that a brain network distributed in the supramodal cortical regions of the frontal, temporal, and parietal lobes plays a central role in conceptual processing. The activation of this network is modulated by two orthogonal dimensions in conceptual processing-the semantic features of individual concepts and the meaningfulness of conceptual combinations-but it remains unclear how the network is functionally organized along these two dimensions. In this fMRI study, we focused on two specific factors, i.e. the social semantic richness of words and the semantic plausibility of word combinations, along the two dimensions. In literature, the distributions of the effects of the two factors are very similar, but have not been rigorously compared in one study. We orthogonally manipulated the two factors in a phrase comprehension task and found a clear dissociation between their effects. The combination of these results with our previous findings reveals three adjacently distributed subnetworks of the supramodal semantic network, associated with the sociality effect, imageability effect, and semantic plausibility effect, respectively. Further analysis of the resting-state functional connectivity data indicated that the functional dissociation among the three subnetworks is associated with their underlying intrinsic connectivity structures.

Coin, telephone, and handcuffs: Neural correlates of social knowledge of inanimate objects.

A variety of objects are made to serve social functions. The use of these objects has greatly enriched and expanded our social behaviors. How do our brains represent the social knowledge of inanimate objects such as coins, telephones, and handcuffs? According to a recent version of the grounded theory, social knowledge of inanimate objects might be grounded in the mentalizing network, as the social functions of inanimate objects are closely associated with the intentions of the people using them. However, there is also evidence that the mentalizing network may only get activated when a human/mental agent is detected. Using fMRI, we explored the neural correlates of social knowledge of inanimate objects by comparing the brain activation evoked by high-sociality object nouns (e.g., banknote) with that evoked by low-sociality object nouns (e.g., battery). The left anterior superior temporal sulcus, a classic part of the mentalizing network, showed higher activation for the high-sociality inanimate object nouns than for the low-sociality ones in the whole-brain analysis. Several other areas of the mentalizing network showed sensitivity to object sociality in small volume correction and/or region-of-interest analyses. Our findings indicate that social knowledge of inanimate objects is supported by brain areas in the mentalizing network.

Color-relation-based capture occurs globally.

Previous studies have shown that a distractor matching the target-nontarget color relation did not capture attention when it appeared outside of the attentional window, indicating that color-relation-based attention is lack of global selection. The present study examined whether a distractor best matching the target-nontarget color relation instead of the target color captured attention outside of the attentional window. The results consistently showed that peripheral distractors best matching the target-nontarget color relation instead of the target color captured attention outside of the attentional window. Additionally, color-relation-matched distractors outweighed target-color-matched distractors in capturing attention under this circumstance. This suggests that the color-relation-based attention shares the hallmark of global selection with the color-based attention. Combined with the previous finding of double dissociation of color-relation-based attention and color-based attention (Du & Jiao, Journal of Experimental Psychology: Human Perception and Performance, 42(4), 480-493, 2016; Du, Yin, Qi, & Zhang, Psychonomic Bulletin & Review, 21(4), 1011-1018, 2014), preference for color-relation within the attentional window and priority for target color outside of the attentional window might be a strategic choice of visual attention.

Neural correlates of three cognitive processes involved in theory of mind and discourse comprehension.

Neuroimaging studies have found that theory of mind (ToM) and discourse comprehension involve similar brain regions. These brain regions may be associated with three cognitive components that are necessarily or frequently involved in ToM and discourse comprehension, including social concept representation and retrieval, domain-general semantic integration, and domain-specific integration of social semantic contents. Using fMRI, we investigated the neural correlates of these three cognitive components by exploring how discourse topic (social/nonsocial) and discourse processing period (ending/beginning) modulate brain activation in a discourse comprehension (and also ToM) task. Different sets of brain areas showed sensitivity to discourse topic, discourse processing period, and the interaction between them, respectively. The most novel finding was that the right temporoparietal junction and middle temporal gyrus showed sensitivity to discourse processing period only during social discourse comprehension, indicating that they selectively contribute to domain-specific semantic integration. Our finding indicates how different domains of semantic information are processed and integrated in the brain and provides new insights into the neural correlates of ToM and discourse comprehension.

Fine Subdivisions of the Semantic Network Supporting Social and Sensory-Motor Semantic Processing.

Neuroimaging studies have consistently indicated that semantic processing involves a brain network consisting of multimodal cortical regions distributed in the frontal, parietal, and temporal lobes. However, little is known about how semantic information is organized and processed within the network. Some recent studies have indicated that sensory-motor semantic information modulates the activation of this network. Other studies have indicated that this network responds more to social semantic information than to other information. Using fMRI, we collectively investigated the brain activations evoked by social and sensory-motor semantic information by manipulating the sociality and imageability of verbs in a word comprehension task. We detected 2 subgroups of brain regions within the network showing sociality and imageability effects, respectively. The 2 subgroups of regions are distinct but overlap in bilateral angular gyri and adjacent middle temporal gyri. A follow-up analysis of resting-state functional connectivity showed that dissociation of the 2 subgroups of regions is partially associated with their intrinsic functional connectivity differences. Additionally, an interaction effect of sociality and imageability was observed in the left anterior temporal lobe. Our findings indicate that the multimodal cortical semantic network has fine subdivisions that process and integrate social and sensory-motor semantic information.

Skipping of Chinese characters does not rely on word-based processing.

Previous eye-movement studies have indicated that people tend to skip extremely high-frequency words in sentence reading, such as "the" in English and "/de" in Chinese. Two alternative hypotheses have been proposed to explain how this frequent skipping happens in Chinese reading: one assumes that skipping happens when the preview has been fully identified at the word level (word-based skipping); the other assumes that skipping happens whenever the preview character is easy to identify regardless of whether lexical processing has been completed or not (character-based skipping). Using the gaze-contingent display change paradigm, we examined the two hypotheses by substituting the preview of the third character of a four-character Chinese word with the high-frequency Chinese character "/de", which should disrupt the ongoing word-level processing. The character-based skipping hypothesis predicts that this manipulation will enhance the skipping probability of the target character (i.e., the third character of the target word), because the character "/de" has much higher character frequency than the original character. The word-based skipping hypothesis instead predicts a reduction of the skipping probability of the target character because the presence of the character "/de" is lexically infelicitous at word level. The results supported the character-based skipping hypothesis, indicating that in Chinese reading the decision of skipping a character can be made before integrating it into a word.

Prenatal findings and molecular cytogenetic analyses of partial trisomy 12q (12q24.32-->qter) and partial monosomy 21q (21q22.2-->qter).

OBJECTIVES: To present the prenatal findings and molecular cytogenetic analyses of partial trisomy 12q and partial monosomy 21q, and a review of the literature. METHODS: Amniocentesis was performed at 23 gestational weeks in a 33-year-old woman because of abnormal sonographic findings. Amniocentesis revealed a derivative chromosome 21, or der(21), with a deletion on the region of 21q22.2 and an addendum of a small chromosomal segment of unknown origin. The maternal karyotype was subsequently found to be 46,XX,t(12;21)(q24.32;q22.2). Level II ultrasound showed microcephaly, micrognathia, a ventricular septal defect, and rocker-bottom feet. The pregnancy was terminated. A malformed infant was delivered without the phenotype of holoprosencephaly (HPE). Fluorescence in situ hybridization (FISH) and polymorphic DNA markers were used to investigate the involved chromosomal segments. RESULTS: FISH study showed the absence of the signal of 21q subtelomeric probe and the presence of the signal of 12q subtelomeric probe in the der(21). The fetal karyotype was 46,XY,der(21) t(12;21)(q24.32;q22.2)mat. Genetic marker analysis showed a deletion at 21q22.2 and a breakpoint between D21S156 (present) and D21S1245 (absent). The deleted segment was measured about 4.5 Mb encompassing the HPE critical region. CONCLUSIONS: Molecular genetic analyses help in determining the prenatally detected unbalanced cryptic translocation as well as parental balanced subtle translocation. A duplication of 12q24.32-->qter and a deletion of 21q22.2-->qter may be associated with prenatal sonographic findings of microcephaly, borderline ventriculomegaly and cerebellar hypoplasia, micrognathia, a ventricular septal defect, and rocker-bottom feet. Haploinsufficiency of the HPE critical region at 21q22.3 may not cause an HPE phenotype.