Limb development genes underlie variation in human fingerprint patterns.

Fingerprints are of long-standing practical and cultural interest, but little is known about the mechanisms that underlie their variation. Using genome-wide scans in Han Chinese cohorts, we identified 18 loci associated with fingerprint type across the digits, including a genetic basis for the long-recognized "pattern-block" correlations among the middle three digits. In particular, we identified a variant near EVI1 that alters regulatory activity and established a role for EVI1 in dermatoglyph patterning in mice. Dynamic EVI1 expression during human development supports its role in shaping the limbs and digits, rather than influencing skin patterning directly. Trans-ethnic meta-analysis identified 43 fingerprint-associated loci, with nearby genes being strongly enriched for general limb development pathways. We also found that fingerprint patterns were genetically correlated with hand proportions. Taken together, these findings support the key role of limb development genes in influencing the outcome of fingerprint patterning.

The effect of health literacy on patient's perceived shared decision-making among Chinese cancer patients.

OBJECTIVES: To explore the relationship between patient's health literacy and perceived shared decision-making (SDM) among Chinese cancer patients. METHODS: A cross-sectional study was conducted involving a convenience sample of 458 cancer patients from four public hospitals in Guangzhou, China. Patients' self-reported data were collected using the Health Literacy Management Scale (HeLMS) and the nine-item Shared Decision-Making Questionnaire (SDM-Q-9). Hierarchical multiple regressions, controlling for patient-doctor relationship, social support, sociodemographic and clinical variables were conducted to explore the effect of health literacy on perceived SDM. RESULTS: Health literacy itself accounted for 68.0% of the variance in perceived SDM. Higher scores in domains "information acquisition ability," and "communication interaction ability" of HeLMS were significantly associated with a higher level of perceived SDM after controlling the covariates (R2  = 75.7%). CONCLUSIONS: Health literacy, especially the information acquisition ability and communication interaction ability, played a prominent role for Chinese cancer patients to be involved in treatment decision making.

Nuclear factor OsNF-YB4 promotes flowering by negatively regulating the floral repressor gene Ghd7 in rice.

Flowering time or heading date is a critical agronomic trait of rice and is regulated by numerous genes, including several genes encoding nuclear factor YB (NF-YB) in rice, NF-YB11 is one of the genes well known to be involved in the process, delaying flowering under long-day (LD) conditions but promoting flowering under short-day (SD) conditions. In this study, we identified another NF-YB gene, OsNF-YB4. Overexpression of OsNF-YB4 promoted rice flowering under both natural long-day (NLD) and natural short-day (NSD) conditions, whereas suppression or loss-of-function of this gene delayed flowering. The transcription of OsNF-YB4 exhibited an obvious circadian pattern and was induced by light under both LD and SD conditions. Expression analyses of flowering regulators in the photoperiodic flowering pathway demonstrated that up-regulation of OsNF-YB4 resulted in down-regulation of floral repressor Grain number, plant height and heading date 7 (Ghd7), and thus activating the Early heading date 1 (Ehd1)-mediated flowering pathway. Besides, OsNF-YB4 was observed to bind to the specific CCAAT-box regions in the Ghd7 promoter in vitro and interact with GHD7 in yeast. All these evidences support that OsNF-YB4 functions as a flowering promoter by negatively regulating the expression of floral repressor Ghd7 in rice photoperiodic flowering-time regulatory network.

Information, deliberation, and decisional control preferences for participation in medical decision-making and its influencing factors among Chinese cancer patients.

BACKGROUND: Patient-centred care should strive to respond to the individual patient's needs and preferences when possible. Yet, preferences of cancer patients for participation in different stages of the medical decision-making process to increase matching of preferred and actual participation of the patients in decision-making are not well known. OBJECTIVE: This study aimed to determine the level of information, deliberation and decisional control preferences in decision-making practices among Chinese cancer patients and to explore their association with the sociodemographic and clinical variables of the patients. METHODS: A cross-sectional study was conducted involving a convenience sample of 328 cancer patients from three public hospitals in Guangzhou, China. The Patient Expectation for Participation in Medical Decision-making Scale (PEPMDS) was used to evaluate information, deliberation and decisional control preferences of the patients. Binary logistic regressions were conducted to determine the association between sociodemographic variables, clinical variables and preferences of the patients. RESULTS: Most patients reported a high preference for information (73.2%) and deliberation (73.8%), while a small number (37.2%) reported a high preference for decisional control. Younger patients and patients with higher levels of education were significantly more likely to have a high preference for information, deliberation and decisional control. Patients with low annual family incomes were significantly more likely to have a low preference for decisional control. CONCLUSION: Preferences of patients for involvement in different stages of decision-making practices could vary. The level of preferences appears to be related to the patient's age, education level, and financial status. PRACTICE IMPLICATIONS: Healthcare providers should tailor the participatory approaches of patients considering individual preferences for information, deliberation and decisional control during medical decision-making. PATIENT CONTRIBUTION: Patients participated in the survey and filled in the questionnaires.

The wild sweetpotato (Ipomoea trifida) genome provides insights into storage root development.

BACKGROUND: Sweetpotato (Ipomoea batatas (L.) Lam.) is the seventh most important crop in the world and is mainly cultivated for its underground storage root (SR). The genetic studies of this species have been hindered by a lack of high-quality reference sequence due to its complex genome structure. Diploid Ipomoea trifida is the closest relative and putative progenitor of sweetpotato, which is considered a model species for sweetpotato, including genetic, cytological, and physiological analyses. RESULTS: Here, we generated the chromosome-scale genome sequence of SR-forming diploid I. trifida var. Y22 with high heterozygosity (2.20%). Although the chromosome-based synteny analysis revealed that the I. trifida shared conserved karyotype with Ipomoea nil after the separation, I. trifida had a much smaller genome than I. nil due to more efficient eliminations of LTR-retrotransposons and lack of species-specific amplification bursts of LTR-RTs. A comparison with four non-SR-forming species showed that the evolution of the beta-amylase gene family may be related to SR formation. We further investigated the relationship of the key gene BMY11 (with identity 47.12% to beta-amylase 1) with this important agronomic trait by both gene expression profiling and quantitative trait locus (QTL) mapping. And combining SR morphology and structure, gene expression profiling and qPCR results, we deduced that the products of the activity of BMY11 in splitting starch granules and be recycled to synthesize larger granules, contributing to starch accumulation and SR swelling. Moreover, we found the expression pattern of BMY11, sporamin proteins and the key genes involved in carbohydrate metabolism and stele lignification were similar to that of sweetpotato during the SR development. CONCLUSIONS: We constructed the high-quality genome reference of the highly heterozygous I. trifida through a combined approach and this genome enables a better resolution of the genomics feature and genome evolutions of this species. Sweetpotato SR development genes can be identified in I. trifida and these genes perform similar functions and patterns, showed that the diploid I. trifida var. Y22 with typical SR could be considered an ideal model for the studies of sweetpotato SR development.

Therapeutic effect and mechanism of electroacupuncture at Zusanli on plasticity of interstitial cells of Cajal: a study of rat ileum.

BACKGROUND: Electroacupuncture (EA) is one of the techniques of acupuncture and is believed to be an effective alternative and complementary treatment in many disorders. The aims of this study were to investigate the effects and mechanisms of EA at acupoint Zusanli (ST36) on the plasticity of interstitial cells of Cajal (ICCs) in partial bowel obstruction. METHODS: A Sprague Dawley rat model of partial bowel obstruction was established and EA was conducted at Zusanli (ST36) and Yinglingquan (SP9) in test and control groups, respectively. Experiments were performed to study the effects and mechanisms of EA at Zusanli on intestinal myoelectric activity, distribution and alteration of ICCs, expression of inflammatory mediators, and c-Kit expression. RESULTS: 1) EA at Zusanli somewhat improved slow wave amplitude and frequency in the partial obstruction rats. 2) EA at Zusanli significantly stimulated the recovery of ICC networks and numbers. 3) the pro-inflammatory mediator TNF-α and NO activity were significantly reduced after EA at Zusanli, However, no significant changes were observed in the anti-inflammatory mediator IL-10 activity. 4) EA at Zusanli re-expressed c-Kit protein. However, EA at the control acupoint, SP9, significantly improved slow wave frequency and amplitude, but had no effect on ICC or inflammatory mediators. CONCLUSIONS: We concluded that EA at Zusanli might have a therapeutic effect on ICC plasticity, and that this effect might be mediated via a decrease in pro-inflammatory mediators and through the c-Kit signaling pathway, but that the relationship between EA at different acupoints and myoelectric activity needs further study.

Determinants of cancer patients' involvement in treatment decision-making based on the COM-B model: A cross-sectional study.

OBJECTIVES: Cancer patients' involvement in treatment decision-making is affected by various factors, with the mechanisms not readily understood. This study explores the underlying mechanisms based on the Capability, Opportunity, Motivation and Behavior (COM-B) model and literature review. METHODS: A cross-sectional survey was conducted and 300 cancer patients conveniently recruited from three tertiary hospitals validly completed the self-administered questionnaires. Structural equation modeling (SEM) approach was used to test the hypothesized model. RESULTS: The findings generally supported the hypothesized model, which could explain 45% of the variance in cancer patients' involvement in treatment decision-making. Cancer patients' health literacy and perceived facilitation of involvement from health professionals had direct and indirect effects on their actual involvement, with the total effect ß = 0.594, ß = 0.223, P < 0.001, respectively. Patients' views of involvement in treatment decision-making had a direct effect on their actual involvement (ß = 0.296, P < 0.001) and completely mediated the relationship between self-efficacy and their actual involvement (ß = 0.040, P < 0.05). CONCLUSIONS: Findings support the COM-B model's explanatory potential in the context of cancer patients' involvement in treatment decision-making.

The Promotion of Humoral Immune Responses in Humans via SOCS1-Mediated Th2-Bias Following SARS-CoV-2 Vaccination.

The effectiveness of SARS-CoV-2 vaccines varies among individuals. During the COVID-19 global pandemic, SARS-CoV-2 infection showed significant Th1 characteristics, suggesting that the immune disorder and production of SARS-CoV-2 antibodies may be related to Th1/Th2 bias. However, the molecular mechanisms underlying Th1/Th2 bias effects on host immune responses to viruses remain unclear. In this study, the top three subjects with the highest and lowest changes in anti-SARS-CoV-2 antibodies after receiving three doses of SARS-CoV-2 vaccination were selected and defined as the elevated group (E) and the control group (C), respectively. Peripheral blood was collected, single-cell sequencing was performed before and after the third dose of the SARS-CoV-2 vaccine, and the changes in T cell clusters were analyzed. Compared with the C group, the Treg pre-vaccination proportion was lower in E, while the post-vaccination proportion was higher, suggesting that Tregs may be crucial in this process. Differential analysis results of Tregs between the two groups revealed that differentially expressed genes (DEGs) were significantly enriched in the IL4 pathway. Correlation analysis between DEGs and serum antibody showed that the expression of NR4A2, SOCS1, and SOCS3 in Tregs was significantly correlated with serum antibodies, suggesting that the immune response in E group changed to Th2 bias, thereby promoting host humoral immune responses. On the other hand, antibody-related genes SOCS1 and NR4A2, as well as lnc-RNA MALAT1 and NEAT1, were highly expressed in the CD4-MALAT1 subclusters. In summary, our study revealed that Th2 bias promotes humoral immune responses in humans by increasing SOCS1 in T cells after SARS-CoV-2 vaccination. Moreover, NR4A2, SOCS1, MALAT1, and NEAT1 were identified as the potential key biomarkers or treatment targets for enhanced SARS-CoV-2 antibody production by influencing the Th1/Th2 balance in T cells. Our findings have important implications for population stratification and tailored therapeutics for more effective SARS-CoV-2 vaccines.

Overexpression of OsNF-YB4 leads to flowering early, improving photosynthesis and better grain yield in hybrid rice.

For cereal crops, such as rice, the grain yield mainly comes from the accumulation of carbohydrates in the seed, which depends ultimately on photosynthesis during the growth period. To create early ripen variety, higher efficiency of photosynthesis is thus necessary to get higher grain yield with shorter growth period. In this study, flowering early was observed in the hybrid rice with overexpression of OsNF-YB4. Along with the flowering early, the hybrid rice also was shorter in plant height with less of leaves and internodes, but no changes of panicle length and leaf emergence. The grain yield was kept or even increased in the hybrid rice with shorter growth period. Transcription analysis revealed that Ghd7-Ehd1-Hd3a/RFT1 was activated early to promote the flowering transition in the overexpression hybrids. RNA-Seq study further showed that carbohydrate-related pathways were significantly altered in addition to circadian pathway. Notably, up-regulation of three pathways related to plant photosynthesis was observed, as well. Increased carbon assimilation with alteration of chlorophyll contents was subsequently detected in the following physiological experiments. All these results demonstrate that overexpression of OsNF-YB4 in the hybrid rice activates flowering early and improves photosynthesis resulting in better grain yield with shorter growth period.

Tryptophan decarboxylase plays an important role in ajmalicine biosynthesis in Rauvolfia verticillata.

Tryptophan decarboxylase (TDC) converts tryptophan into tryptamine that is the indole moiety of ajmalicine. The full-length cDNA of Rauvolfia verticillata (RvTDC) was 1,772 bps that contained a 1,500-bp ORF encoding a 499-amino-acid polypeptide. Recombinant 55.5 kDa RvTDC converted tryptophan into tryptamine. The K (m) of RvTDC for tryptophan was 2.89 mM, higher than those reported in other TIAs-producing plants. It demonstrated that RvTDC had lower affinity to tryptophan than other plant TDCs. The K (m) of RvTDC was also much higher than that of strictosidine synthase and strictosidine glucosidase in Rauvolfia. This suggested that TDC might be the committed-step enzyme involved in ajmalicine biosynthesis in R. verticillata. The expression of RvTDC was slightly upregulated by MeJA; the five MEP pathway genes and SGD showed no positive response to MeJA; and STR was sharply downregulated by MeJA. MeJA-treated hairy roots produced higher level of ajmalicine (0.270 mg g(-1) DW) than the EtOH control (0.183 mg g(-1) DW). Highest RvTDC expression level was detected in hairy root, about respectively 11, 19, 65, and 109-fold higher than in bark, young leaf, old leaf, and root. Highest ajmalicine content was also found in hairy root (0.249 mg g(-1) DW) followed by in bark (0.161 mg g(-1) DW) and young leaf (0.130 mg g(-1) DW), and least in root (0.014 mg g(-1) DW). Generally, the expression level of RvTDC was positively consistent with the accumulation of ajmalicine. Therefore, it could be deduced that TDC might be the key enzyme involved in ajmalicine biosynthesis in Rauvolfia.

Genomic Characterization of a Tomato Yellow Mottle-Associated Virus Collected from a Field Tomato Plant in Chengdu, Southwestern China.

Here, we report the genomic sequence and genetic variations of a Tomato yellow mottle-associated virus. The virus isolated from a field tomato (Solanum lycopersicum) plant in Chengdu, southwestern China, was sequenced via both Illumina and Sanger technologies. Phylogeny indicates that its genome is close to the reported virus sequence from S. lycopersicum collected in 2013 but far from Solanum nigrum collected in 2020.

Genome-Wide Identification and Expression Analysis of Expansin Gene Family in the Storage Root Development of Diploid Wild Sweetpotato Ipomoea trifida.

Expansins play important roles in root growth and development, but investigation of the expansin gene family has not yet been reported in Ipomoea trifida, and little is known regarding storage root (SR) development. In this work, we identified a total of 37 expansins (ItrEXPs) in our previously reported SR-forming I. trifida strain Y22 genome, which included 23 ItrEXPAs, 4 ItrEXPBs, 2 ItrEXLAs and 8 ItrEXLBs. The phylogenetic relationship, genome localization, subcellular localization, gene and protein structure, promoter cis-regulating elements, and protein interaction network were systematically analyzed to reveal the possible roles of ItrEXPs in the SR development of I. trifida. The gene expression profiling in Y22 SR development revealed that ItrEXPAs and ItrEXLBs were down-regulated, and ItrEXPBs were up-regulated while ItrEXLAs were not obviously changed during the critical period of SR expansion, and might be beneficial to SR development. Combining the tissue-specific expression in young SR transverse sections of Y22 and sweetpotato tissue, we deduced that ItrEXLB05, ItrEXLB07 and ItrEXLB08 might be the key genes for initial SR formation and enlargement, and ItrEXLA02 might be the key gene for root growth and development. This work provides new insights into the functions of the expansin gene family members in I. trifida, especially for EXLA and EXLB subfamilies genes in SR development.

An additional whole-exome sequencing study in 102 panel-undiagnosed patients: A retrospective study in a Chinese craniosynostosis cohort.

Craniosynostosis (CRS) is a disease with prematurely fused cranial sutures. In the last decade, the whole-exome sequencing (WES) was widely used in Caucasian populations. The WES largely contributed in genetic diagnosis and exploration on new genetic mechanisms of CRS. In this study, we enrolled 264 CRS patients in China. After a 17-gene-panel sequencing designed in the previous study, 139 patients were identified with pathogenic/likely pathogenic (P/LP) variants according to the ACMG guideline as positive genetic diagnosis. WES was then performed on 102 patients with negative genetic diagnosis by panel. Ten P/LP variants were additionally identified in ten patients, increasing the genetic diagnostic yield by 3.8% (10/264). The novel variants in ANKH, H1-4, EIF5A, SOX6, and ARID1B expanded the mutation spectra of CRS. Then we designed a compatible research pipeline (RP) for further exploration. The RP could detect all seven P/LP SNVs and InDels identified above, in addition to 15 candidate variants found in 13 patients with worthy of further study. In sum, the 17-gene panel and WES identified positive genetic diagnosis for 56.4% patients (149/264) in 16 genes. At last, in our estimation, the genetic testing strategy of "Panel-first" saves 24.3% of the cost compared with "WES only", suggesting the "Panel-first" is an economical strategy.

Characterization and Evaluation of Transgenic Rice Pyramided with the Pi Genes Pib, Pi25 and Pi54.

BACKGROUND: Emergence of new pathogen strains of Magnaporthe oryzae is a major reason for recurrent failure of the resistance mediated by a single resistance gene (Pi) in rice. Stacking various Pi genes in the genome through marker-assisted selection is thus an effective strategy in rice breeding for achieving durable resistance against the pathogen. However, the effect of pyramiding of multiple Pi genes using transgenesis still remains largely unknown. RESULTS: Three Pi genes Pib, Pi25 and Pi54 were transferred together into two rice varieties, the indica variety Kasalath and the japonica variety Zhenghan 10. Transgenic plants of both Kasalath and Zhenghan 10 expressing the Pi transgenes showed imparted pathogen resistance. All the transgenic lines of both cultivars also exhibited shorter growth periods with flowering 2-4 days early, and shorter plant heights with smaller panicle. Thus, pyramiding of the Pi genes resulted in reduced grain yields in both rice cultivars. However, tiller numbers and grain weight were generally similar between the pyramided lines and corresponding parents. A global analysis of gene expression by RNA-Seq suggested that both enhancement and, to a lesser extent, inhibition of gene transcription occurred in the pyramided plants. A total of 264 and 544 differentially expressed genes (DEGs) were identified in Kasalath and Zhenghan 10, respectively. Analysis of the DEGs suggested that presence of the Pi transgenes did not alter gene expression only related to disease resistance, but also impacted many gene transcriptions in the pathways for plant growth and development, in which several were common for both Kasalath and Zhenghan 10. CONCLUSION: Pyramiding of the Pi genes Pib, Pi25 and Pi54 via transgenesis is a potentially promising approach for improving rice resistance to the pathogen Magnaporthe oryzae. However, pleiotropic effects of the Pi genes could potentially result in yield loss. These findings support the idea that immunity is often associated with yield penalties. Rational combination of the Pi genes based on the genetic background may be important to balance yield and disease resistance.

Association of prenatal exposure to phenols and parabens with birth size: A systematic review and meta-analysis.

Phenols and parabens are endocrine-disrupting chemicals and are widely used in daily life products due to their antibacterial action. Previous studies suggest associations of prenatal exposure to phenols and parabens with fetal development; however, such findings are rare and inconsistent. The aim of this review and meta-analysis is to estimate the associations between maternal exposure to phenols and parabens and birth size. We identified 21 relevant studies that met the inclusion criteria through databases of PubMed, Cochrane, EMBASE and Qvid Medline. The last search was in July 3, 2019. The heterogeneity and possibility of publication bias among included studies were assessed by Q-statistic and Begg's test, respectively. Meta-analysis revealed that prenatal exposure to triclosan [number of studies (n) = 12, regression coefficient (ß) = -0.04 g; 95% confidence interval (CI): -0.139, 0.059], benzophenone-3 (n = 10, ß = -0.001 g; 95% CI: -0.013, 0.012), bisphenol A (n = 9, ß = -0.049 g; 95% CI: -0.199, 0.101), 2-4-dichlorophenols (n = 6, ß = -14.124 g; 95% CI: -29.971, 1.723), 2-5-dichlorophenols (n = 6, ß = -0.061 g; 95% CI: -0.196, 0.074) and parabens were negatively associated with fetal birth weight. Most of them were insignificant. Inconsistent and insignificant associations were detected between exposure to phenols and parabens and other birth outcomes. Subgroup analysis suggested that heterogeneity in our meta-analysis was mainly attributed to the studies conducted in developed countries and samples collected in the second trimester. Insignificant and controversial associations of maternal exposure to phenols and parabens with birth size were observed in our study. The study design and methods of the included studies are inconsistent, and the effects of environmental pollutants on human health are complex. Further cohort studies with large samples and a consistent approach are thus required to evaluate the associations of maternal exposure to phenols and parabens with birth size.