Genome-wide association study identifies a gene responsible for temperature-dependent rice germination.

Environment is an important determinant of agricultural productivity; therefore, crops have been bred with traits adapted to their environment. It is assumed that the physiology of seed germination is optimised for various climatic conditions. Here, to understand the genetic basis underlying seed germination, we conduct a genome-wide association study considering genotype-by-environment interactions on the germination rate of Japanese rice cultivars under different temperature conditions. We find that a 4 bp InDel in one of the 14-3-3 family genes, GF14h, preferentially changes the germination rate of rice under optimum temperature conditions. The GF14h protein constitutes a transcriptional regulatory module with a bZIP-type transcription factor, OREB1, and a florigen-like protein, MOTHER OF FT AND TFL 2, to control the germination rate by regulating abscisic acid (ABA)-responsive genes. The GF14h loss-of-function allele enhances ABA signalling and reduces the germination rate. This allele is found in rice varieties grown in the northern area and in modern cultivars of Japan and China, suggesting that it contributes to the geographical adaptation of rice. This study demonstrates the complicated molecular system involved in the regulation of seed germination in response to temperature, which has allowed rice to be grown in various geographical locations.

Sensory Reinnervation With Subcutaneously Embedded Innervated Flaps: An Experimental Study in Rats.

BACKGROUND: In breast reconstruction, both aesthetic outcomes and sensory function are important for postoperative quality of life. Innervated flaps are useful in reconstruction after conventional mastectomy (CM), which leaves a large portion of the skin paddle exposed on the body surface. However, whether they are also useful in skin-sparing mastectomy (SSM) and nipple-sparing mastectomy (NSM) remains unclear. This study aimed to examine the usefulness of innervated flaps in restoring sensation after SSM and NSM using a rat model. METHODS: Dorsal cutaneous nerves of rats were entirely eliminated except for the medial branch of the dorsal cutaneous nerve of thoracic segment 13, resulting in an innervated field surrounded by a denervated field. The innervated field was elevated as an innervated island flap and then subcutaneously embedded, with the skin paddle deepithelialized entirely (NSM group, n = 5) or except at the center (SSM group, n = 6). In the control model (CM group, n = 5), the flap was sutured back into its original position. Postoperative changes in the mechanonociceptive field were evaluated using the cutaneous trunci muscle reflex test. Immunohistochemical evaluation of regenerated nerves in the new mechanonociceptive field was performed at postoperative week 12. RESULTS: In the SSM and CM groups, the mechanonociceptive field expanded around the skin paddle. In the NSM group, a new mechanonociceptive field appeared at postoperative week 4 and expanded thereafter. Areas of the mechanonociceptive field at postoperative week 12 did not differ significantly between the SSM and NSM groups, but were significantly smaller compared with the CM group and comparable to original flap areas. Histologically, S100- and PGP9.5-positive nerve fibers were observed in the dermis of the new mechanonociceptive field and subcutaneous flap tissue. CONCLUSIONS: Subcutaneously embedded innervated island flaps induced nerve regeneration and sensory reinnervation of the denervated skin, suggesting that innervated flaps may also be useful in reconstruction post-SSM/NSM.

Potential of rice landraces with strong culms as genetic resources for improving lodging resistance against super typhoons.

It is generally believed that rice landraces with long culms are susceptible to lodging, and have not been utilized for breeding to improve lodging resistance. However, little is known about the structural culm strength of landraces and their beneficial genetic loci. Therefore, in this study, genome-wide association studies (GWAS) were performed using a rice population panel including Japanese rice landraces to identify beneficial loci associated with strong culms. As a result, the landraces were found to have higher structural culm strength and greater diversity than the breeding varieties. Genetic loci associated with strong culms were identified, and it was demonstrated that haplotypes with positive effects of those loci were present in a high proportion of these landraces. These results indicated that the utilization of the strong culm-associated loci present in Japanese rice landraces may further improve the lodging resistance of modern breeding varieties that have relied on semi-dwarfism.

Growth and Nitrate Reductase Activity Are Impaired in Rice Osnlp4 Mutants Supplied with Nitrate.

Nitrate is an important nutrient and signaling molecule in plants, which modulates the expression of many genes and regulates plant growth. In paddy-grown rice (Oryza sativa), nitrogen is mostly supplied in the form of ammonium but can also be supplied in the form of nitrate. Several nitrogen transporters and nitrate assimilation enzymes have been identified and functionally characterized in rice. However, little is known regarding the nitrate sensing system in rice, and the regulatory mechanisms of nitrate-related genes remain to be elucidated. In recent years, NIN-like proteins (NLPs) have been described as key transcription factors of nitrogen responses in Arabidopsis thaliana, which implies that OsNLP4 is involved in the regulation of nitrate assimilation and nitrogen use efficiency in rice. Here, we show that OsNLP4 can influence plant growth by affecting nitrate reductase (NR) activity. The growth of OsNLP4 knockdown mutants was reduced when nitrate was supplied, but not when ammonium was supplied. The nitrate concentration was significantly reduced in osnlp4 mutants. Furthermore, the concentrations of iron and molybdenum, essential elements for NR activity, were reduced in OsNLP4 knockdown mutants. We propose that, in addition to the regulation of gene expression within the nitrate signaling pathway, OsNLP4 can affect the NR activity and nitrate-dependent growth of rice. Our results support a working model for the role of OsNLP4 in the nitrate signaling pathway.

Targeted sensory reinnervation by direct neurotization of skin: An experimental study in rats.

BACKGROUND: No effective methods currently exist for breast neurotization in implant-based breast reconstruction. Here, we focused on direct neurotization (DN), in which axons regenerating from nerve stumps are directed to the mastectomy flap and aimed to assess whether DN can generate a new mechano-nociceptive field using a rat model of back skin sensory denervation. METHODS: Dorsal cutaneous nerves (DCNs) of rats were exposed and transected, leaving only the left medial branch of the DCN of thoracic segment 13 (mDCN-T13) intact. This procedure resulted in an isolated innervated field surrounded by a denervated field. The mDCN-T13 was transected, and the proximal nerve stump was sutured to the subdermis (DN subdermal group, n = 6) or dermis (DN dermal group, n = 5) of a different region of the denervated field. In the Crush group (n = 5), the intact mDCN-T13 was only crushed. We evaluated the generation of a new mechano-nociceptive field over time using the cutaneous trunci muscle (CTM) reflex test and histomorphometrically evaluated regenerating nerves in the reinnervated region. RESULTS: In the DN groups, the CTM reflex appeared in the DN area after postoperative week 4. The new mechano-nociceptive field gradually expanded afterwards, and by postoperative week 12, the area was substantially larger than the original region innervated by the mDCN-T13 in the DN dermal group, although not as large as that in the Crush group. In histomorphometric evaluations, many S100-positive myelinated fibers were observed in the dermis of the reinnervated area for all groups. CONCLUSION: In targeted sensory reinnervation, DN of the skin is revolutionary in that it allows a new innervated area to be generated at a desired location regardless of whether a distal nerve stump is available. DN may present an effective approach for breast neurotization in breast reconstruction after mastectomy, particularly for procedures that cannot use sensate flaps such as implant-based breast reconstruction.

Construction and integration of three de novo Japanese human genome assemblies toward a population-specific reference.

The complete human genome sequence is used as a reference for next-generation sequencing analyses. However, some ethnic ancestries are under-represented in the reference genome (e.g., GRCh37) due to its bias toward European and African ancestries. Here, we perform de novo assembly of three Japanese male genomes using > 100× Pacific Biosciences long reads and Bionano Genomics optical maps per sample. We integrate the genomes using the major allele for consensus and anchor the scaffolds using genetic and radiation hybrid maps to reconstruct each chromosome. The resulting genome sequence, JG1, is contiguous, accurate, and carries the Japanese major allele at most loci. We adopt JG1 as the reference for confirmatory exome re-analyses of seven rare-disease Japanese families and find that re-analysis using JG1 reduces total candidate variant calls versus GRCh37 while retaining disease-causing variants. These results suggest that integrating multiple genomes from a single population can aid genome analyses of that population.

Fat-augmented latissimus dorsi myocutaneous flap for total breast reconstruction: A report of 54 consecutive Asian cases.

Immediate fat grafting to the latissimus dorsi myocutaneous (LD) flaps is a breakthrough that addresses the issue of insufficient volume of LD. However, the use of this procedure in Asian patients has not yet been reported. Retrospective chart reviews were conducted on 54 Japanese cases of total breast reconstruction using fat-augmented LD flaps at our hospital from September 2017 to June 2019. There were 24 immediate reconstruction cases, 18 immediate two-stage reconstruction cases, nine delayed reconstruction cases, and three delayed two-stage reconstruction cases. Median age was 46 years (range, 29-69 years), and median body mass index was 21.5 (17-33.8). Median mastectomy specimen and flap weight was 225 g (123-993) and 225 g (130-796), respectively. The median volume of fat graft was 114 ml (46-305) for the LD flap and 58 ml (15-200) for the pectoralis major muscle. Of the 53 completed reconstruction cases, 38 (71.7%) achieved sufficient volume with the initial operation and six (11.3%) required additional fat grafting. The proportion of cases in the immediate reconstruction group, which achieved sufficient volume in the initial operation was significantly higher than those of the other three reconstruction groups (p = 0.007). Total breast reconstruction with fat-augmented LD flaps is a viable procedure for thin patients who have insufficient abdominal tissue, for those who wish to avoid abdominal scars, and for those in whom abdominal flaps have already been used. The procedure allows for large volume transplantation even with small skin paddles, which allows for smaller skin paddles to be designed without the need for extensive subcutaneous dissection.

Landraces of temperate japonica rice have superior alleles for improving culm strength associated with lodging resistance.

Lodging can reduce grain yield and quality in cereal crops including rice (Oryza sativa L.). To achieve both high biomass production and lodging resistance, the breeding of new cultivars with strong culms is a promising strategy. However, little is known about the diversity of culm strength in temperate japonica rice and underlying genetic factors. Here, we report a wide variation of culm strength among 135 temperate japonica cultivars, and some landraces having the strongest culms among these cultivars. The genome-wide association study (GWAS) identified 55 quantitative trait loci for culm strength and morphological traits, and revealed several candidate genes. The superior allele of candidate gene for culm thickness, OsRLCK191, was found in many landraces but had not inherited to the modern improved cultivars. Our results suggest that landraces of temperate japonica rice have unutilized superior alleles for contributing future improvements of culm strength and lodging resistance.

A Simple and Scarless Method for Inframammary Fold Correction Using a Barbed Suture.

BACKGROUND: In the typical procedure for secondary correction of the inframammary fold (IMF) following breast reconstruction, a large incision is often required, and this increases surgical invasiveness. The "drawstring method" is a simple procedure for recreating a smooth IMF. We modified the drawstring method and developed an essentially scarless method for IMF correction from small stab incisions. METHODS: Patients at our hospital who presented with IMF ptosis or loss of definition after breast reconstruction and required IMF correction, as well as those who requested IMF recreation for the contralateral breast, during the period spanning May 2016 to June 2019 were considered for this study. We collected and analyzed demographic data, as well as complications and postoperative outcomes. RESULTS: The new method was performed on 20 patients, with the following breakdown: IMF recreation after breast reconstruction with a deep inferior epigastric artery perforator flap (11 patients), IMF recreation after breast reconstruction with a breast implant (2 patients), IMF recreation after breast reconstruction with fat graft (5 patients), and IMF recreation for the contralateral breast (2 patients). Overcorrection of the IMF stabilized by 2-3 months postoperatively, resulting in a smooth and well-defined IMF. For non-breast implant cases, the implant volume increased at the lower pole. Slack in the suture was observed in only 2 patients of the deep inferior epigastric artery perforator group and in 1 patient of the breast implant group after 6 months postoperatively. CONCLUSIONS: Our new method allows for the recreation of an essentially scarless, smooth, and well-defined IMF. IMF definition can be adjusted by altering the depth of the barbed suture. Since this method can be performed under local anesthesia, it offers the benefits of reducing medical costs and physical burden on patients.

Genome-wide expression quantitative trait locus studies facilitate isolation of causal genes controlling panicle structure.

The morphology of rice (Oryza sativa L.) panicles is an important determinant of grain yield, and elucidation of the genetic control of panicle structure is very important for fulfilling the demand for high yield in breeding programs. In a quantitative trait locus (QTL) study using 82 backcross inbred lines (BILs) derived from Koshihikari and Habataki, 68 QTLs for 25 panicle morphological traits were identified. Gene expression profiling from inflorescence meristems of BILs was obtained. A combination of phenotypic QTL (pQTL) and expression QTL (eQTL) analysis revealed co-localization between pQTLs and eQTLs, consistent with significant correlations between phenotypic traits and gene expression levels. By combining pQTL and eQTL data, two genes were identified as controlling panicle structure: OsMADS18 modulates the average length of the primary rachis and OsFTL1 has pleiotropic effects on the total number of secondary rachides, number of grains per panicle, plant height and the length of flag leaves. Phenotypes were confirmed in RNA interference knocked-down plants and overexpressor lines. The combination of pQTL and eQTL analysis could facilitate identification of genes involved in rice panicle formation.

The Japanese Breast Cancer Society clinical practice guidelines for surgical treatment of breast cancer, 2018 edition.

We have prepared the Japanese Breast Cancer Society clinical practice guidelines (CPGs) for surgical treatment of breast cancer, 2018 update after a systematic review (SR) of the literature based upon the Medical Information Network Distribution Service (Minds) procedure. The CPG committee for surgical treatment of breast cancer, composed of breast surgeons and plastic surgeons treating breast cancer, has developed the CPGs. Eight clinical questions (CQs) were selected and divided roughly into the following five categories: (1) breast surgery in initial therapy (CQs 1-3); (2) axillary surgery in initial therapy (CQs 4-5); (3) breast reconstruction in initial therapy (CQ 6); (4) surgical treatment for recurrent and metastatic breast cancer (CQs 7-8); and (5) others. Recommendations for these CQs were decided by the GRADE grid method. In addition, 4 outlines, 14 background questions (BQs), and 12 future research questions (FQs) were also selected. Statements for these BQs and FQs are provided. We developed the updated CPGs for surgical treatment of breast cancer, 2018, which include 8 CQs and recommendations. As a decision-making tool for the understanding and treatment of breast cancer, these guidelines will help surgical oncologists dealing with breast cancer, medical staff, and patients, along with their family members.

GWAS with principal component analysis identifies a gene comprehensively controlling rice architecture.

Elucidation of the genetic control of rice architecture is crucial due to the global demand for high crop yields. Rice architecture is a complex trait affected by plant height, tillering, and panicle morphology. In this study, principal component analysis (PCA) on 8 typical traits related to plant architecture revealed that the first principal component (PC), PC1, provided the most information on traits that determine rice architecture. A genome-wide association study (GWAS) using PC1 as a dependent variable was used to isolate a gene encoding rice, SPINDLY (OsSPY), that activates the gibberellin (GA) signal suppression protein SLR1. The effect of GA signaling on the regulation of rice architecture was confirmed in 9 types of isogenic plant having different levels of GA responsiveness. Further population genetics analysis demonstrated that the functional allele of OsSPY associated with semidwarfism and small panicles was selected in the process of rice breeding. In summary, the use of PCA in GWAS will aid in uncovering genes involved in traits with complex characteristics.

Shaping a Flap Using a Bioabsorbable Mold-A Preliminary Report.

BACKGROUND: We previously reported that good surgical outcomes can be obtained with breast mold made by 3-dimensional printing. However, detailed breast shape is often difficult to create. Accordingly, we aimed to determine whether transplanting a flap and bioabsorbable mold in vivo would yield better results by retaining the flap shape inside the mold during the scar formation period. METHODS: Vascularized adipose flaps were elevated in the bilateral inguinal region of male Sprague-Dawley rats (n = 7). A cone-shaped, bioabsorbable mold (LactoSorb mesh) was created using a template. On the experimental side, the flap was inserted into the mold and fixed. On the control side, a conical flap was created using absorbable sutures, based on a template. RESULTS: The flaps were harvested 3 months postoperatively, and flap volume, base area, and projection were measured with 3-dimensional imaging. Volume and base area on the mold side tended to be smaller than those on the control side (P = 0.18 and 0.13, respectively) and close to the values of the template. In addition, the ratio of projection and base area value was significantly greater on the mold side than on the control side (P = 0.04). Histology revealed little inflammatory cell invasion, and scar tissue thickness around the flap showed no significant difference between the 2 groups (P = 0.76). CONCLUSIONS: This study demonstrated that soft-tissue morphology can be controlled to some extent with a bioabsorbable mold. Its clinical application in breast reconstruction requires further investigation.

Efficacy of STRATAFIX in Inframammary Fold Recreation in Autologous Breast Reconstruction.

Supplemental Digital Content is available in the text.

Staged Prosthetic Reconstruction with Fat Grafting for Severe Depressive Breast Deformation after Breast-conserving Therapy.

Breast-conserving therapy, where radiotherapy is performed after partial mastectomy, is a widely used surgical method that can preserve most of the breast tissue without increasing the recurrence rate of breast cancer. However, without reconstruction, asymmetry of the breast occurs due to the tissue defect and radiation fibrosis, producing in poor cosmetic results. In this case study, we performed staged prosthetic breast reconstruction combined with fat grafting for severe depressive deformation of the breast after breast-conserving therapy. The first surgery involved insertion of a tissue expander and fat grafting, second surgery was the reduction of injected saline volume and fat grafting, and third surgery involved exchange for an implant and fat grafting. The skin in the depressed area, which had atrophied, became soft and flexible; deformation was also improved, and the patient was satisfied with the aesthetic outcome. It is expected that fat grafting will fertilize and qualitatively improve the damaged tissue due to irradiation, reducing the complications related to the tissue expander and implant. We believe that it will be possible to correct a breast deformity after breast-conserving therapy using a tissue expander and implant, which had not been considered as a solution. The results showed that the present method can be an option for delayed reconstruction after breast-conserving therapy.

Time-Course Transcriptomics Analysis Reveals Key Responses of Submerged Deepwater Rice to Flooding.

Water submergence is an environmental factor that limits plant growth and survival. Deepwater rice (Oryza sativa) adapts to submergence by rapidly elongating its internodes and thereby maintaining its leaves above the water surface. We performed a comparative RNA sequencing transcriptome analysis of the shoot base region, including basal nodes, internodes, and shoot apices of seedlings at two developmental stages from two varieties with contrasting deepwater growth responses. A transcriptomic comparison between deepwater rice cv C9285 and nondeepwater rice cv Taichung 65 revealed both similar and differential expression patterns between the two genotypes during submergence. The expression of genes related to gibberellin biosynthesis, trehalose biosynthesis, anaerobic fermentation, cell wall modification, and transcription factors that include ethylene-responsive factors was significantly different between the varieties. Interestingly, in both varieties, the jasmonic acid content at the shoot base decreased during submergence, while exogenous jasmonic acid inhibited submergence-induced internode elongation in cv C9285, suggesting that jasmonic acid plays a role in the submergence response of rice. Furthermore, a targeted de novo transcript assembly revealed transcripts that were specific to cv C9285, including submergence-induced biotic stress-related genes. Our multifaceted transcriptome approach using the rice shoot base region illustrates a differential response to submergence between deepwater and nondeepwater rice. Jasmonic acid metabolism appears to participate in the submergence-mediated internode elongation response of deepwater rice.

Screening Arabidopsis thaliana mutants for low sensitivity to manganese identifies novel alleles of NRAMP1 and PGSIP6.

Manganese (Mn) is an essential micronutrient; however, few genes required for growth under low-Mn conditions have been identified. In this study, we isolated Arabidopsis thaliana mutants sensitive to low-Mn conditions from ethyl methanesulfonate-mutagenized seeds. Among them, we identified the causal genes of two mutants. One mutant (35-34) exhibited a short root phenotype and low Mn concentration in the shoots. The other mutant (30-11) exhibited a small shoot phenotype with Mn concentrations similar to the control. Genetic mapping, allelism tests, and gene complementation tests identified the causal genes as At1g80830 (NRAMP1) for 35-34 and At5g18480 (PGSIP6) for 30-11. NRAMP1 was previously reported to be essential for Mn uptake under low-Mn conditions, thus validating our screening method. PGSIP6 encodes inositol phosphorylceramide glucuronosyltransferase, which is involved in glycosyl inositol phosphorylceramide sphingolipid glycosylation. PGSIP6-green fluorescent protein was localized to the Golgi apparatus, which is consistent with its function in the glycosylation of sphingolipids. Our screening identified a novel gene required for low-Mn tolerance, and we also provide new insights towards understanding the physiological function of PGSIP6.