Genomic basis of multiphase evolution driving divergent selection of zinc-finger homeodomain genes.

Gene families divergently evolve and become adapted as different genes with specific structures and functions in living organisms. We performed comprehensive structural and functional analyses of Zinc-finger homeodomain genes (ZF-HDs), including Mini zinc-finger genes (MIFs) and Zinc-finger with homeodomain genes (ZHDs), displaying competitive functions each other. Intensive annotation updates for 90 plant genomes verified that most MIFs (MIF-Is) exhibited distinct motif compositions from ZHDs, although some MIFs (MIF-Zs) contained ZHD-specific motifs. Phylogenetic analyses suggested that MIF-Zs and ZHDs originated from the same ancestral gene, whereas MIF-Is emerged from a distinct progenitor. We used a gene-editing system to identify a novel function of MIF-Is in rice: regulating the surface material patterns in anthers and pollen through transcriptional regulation by interacting ZHDs. Kingdom-wide investigations determined that (i) ancestral MIFs diverged into MIF-Is and MIF-Zs in the last universal common ancestor, (ii) integration of HD into the C-terminal of MIF-Zs created ZHDs after emergence of green plants and (iii) MIF-Is and ZHDs subsequently expanded independently into specific plant lineages, with additional formation of MIF-Zs from ZHDs. Our comprehensive analysis provides genomic evidence for multiphase evolution driving divergent selection of ZF-HDs.

Comparative and expression analyses of AP2/ERF genes reveal copy number expansion and potential functions of ERF genes in Solanaceae.

BACKGROUND: The AP2/ERF gene family is a superfamily of transcription factors that are important in the response of plants to abiotic stress and development. However, comprehensive research of the AP2/ERF genes in the Solanaceae family is lacking. RESULTS: Here, we updated the annotation of AP2/ERF genes in the genomes of eight Solanaceae species, as well as Arabidopsis thaliana and Oryza sativa. We identified 2,195 AP2/ERF genes, of which 368 (17%) were newly identified. Based on phylogenetic analyses, we observed expansion of the copy number of these genes, especially those belonging to specific Ethylene-Responsive Factor (ERF) subgroups of the Solanaceae. From the results of chromosomal location and synteny analyses, we identified that the AP2/ERF genes of the pepper (Capsicum annuum), the tomato (Solanum lycopersicum), and the potato (Solanum tuberosum) belonging to ERF subgroups form a tandem array and most of them are species-specific without orthologs in other species, which has led to differentiation of AP2/ERF gene repertory among Solanaceae. We suggest that these genes mainly emerged through recent gene duplication after the divergence of these species. Transcriptome analyses showed that the genes have a putative function in the response of the pepper and tomato to abiotic stress, especially those in ERF subgroups. CONCLUSIONS: Our findings will provide comprehensive information on AP2/ERF genes and insights into the structural, evolutionary, and functional understanding of the role of these genes in the Solanaceae.

Short-term effect of growth hormone treatment in childhood leukemia survivors with growth hormone deficiency.

PURPOSE: Survivors of childhood leukemia are at risk of growth impairment due to intensive chemotherapy and radiation treatments. This study investigated the auxological and biochemical characteristics of childhood leukemia survivors diagnosed with growth hormone deficiency (GHD) and the changes in these parameters after 1 year of growth hormone (GH) treatment. METHODS: A total of 24 children diagnosed with GHD after leukemia treatment was analyzed. Clinical and biochemical data were collected retrospectively at leukemia diagnosis, GHD diagnosis, and 1 year after GH treatment. Standard deviation score (SDS) was calculated based on the age- and gender-adjusted population. RESULTS: Of the 24 children included in this study, 19 received GH treatment. The median age at GHD diagnosis was 12.3 years, and the median delay in bone age was 1.46 years. Height SDS decreased from -0.69 at leukemia diagnosis to -2.58 at GHD diagnosis (P<0.001). The change in height SDS with and without GH for 1 year was 0.35 and -0.21, respectively (P=0.044). In regression analyses, higher height SDS at GHD diagnosis and a smaller decrease of the height SDS between leukemia and GHD diagnoses were positively correlated with height SDS after GH treatment. CONCLUSION: GH treatment could be beneficial and safe for improving height in childhood leukemia survivors with GHD. Height SDS at GHD diagnosis and reduction of height SDS between leukemia and GHD diagnosis could be potential factors in predicting the therapeutic effects. Close auxological monitoring is recommended for any childhood leukemia survivors who experience posttreatment height decline.

Factors affecting bone mineral density in children and adolescents with secondary osteoporosis.

PURPOSE: This study aimed to investigate the clinical factors associated with bone mineral density (BMD) among children and adolescents with osteoporosis secondary to treatment for underlying clinical conditions. METHODS: We retrospectively reviewed the medical records of patients aged 10-18 years and evaluated them for lumbar spine BMD (LSBMD) after treatment for underlying diseases, including hemato-oncologic, rheumatologic system, and inflammator y bowel diseases. LSBMD measured by dual-energy x-ray absorptiometry (DXA) performed from March 2019 to March 2021 was evaluated. We analyzed 117 patients who underwent initial DXA after treatment for underlying diseases. RESULTS: Subjects in this study had multiple underlying diseases: hemato-oncologic (78.6%), rheumatologic (11.1%), and inflammatory bowel diseases (10.3%). There was no significant association between the z-score and bone metabolic markers (P>0.05). However, higher cumulative glucocorticoid (GC) dose significantly reduced LSBMD z-score (P=0.029). Moreover, the association between cumulative dose of GC and initial z-score of LSBMD was significant in logarithmic regression analysis (P=0.003, R2=0.149). GC accumulation was a significant risk factor for vertebral fracture when the initial BMD was evaluated after treatment (P=0.043). Bone metabolic markers did not significantly influence the risk of vertebral fracture. CONCLUSION: Initial bone mass density of the lumbar spine evaluated after long-term GC use for underlying diseases is a predictor of further vertebral fractures.

Effect of Growth Hormone Therapy on a 4-Year-Old Girl with Pfeiffer Syndrome and Short Stature: A Case Report.

Fibroblast growth factor receptors (FGFRs) are expressed in epiphyseal cartilage cells of developing bones and regulate endochondral bone formation with interdependent signaling pathways. Gene mutation in FGFRs disrupts the formation of endochondral bony structure by reducing the number of proliferating chondrocytes. Among the syndromes caused by mutation in the FGFR gene, Pfeiffer syndrome is a rare inherited disease characterized by acrocephalosyndactyly related to hypertelorism, broad pollex, and hallux. We describe the case of a 4-year-old girl with short stature, advanced bone age, wide thumbs and great toes. The patient was diagnosed with partial growth hormone deficiency and an identified mutation in the FGFR2 gene. Standard deviation score of her height increased after starting growth hormone therapy. This report will raise awareness of the growth hormone provocation test regardless of bone age in patients with short stature founded FGFR gene mutation.

Identification of novel PHD-finger genes in pepper by genomic re-annotation and comparative analyses.

BACKGROUND: The plant homeodomain (PHD)-finger gene family that belongs to zinc-finger genes, plays an important role in epigenetics by regulating gene expression in eukaryotes. However, inaccurate annotation of PHD-finger genes hinders further downstream comparative, evolutionary, and functional studies. RESULTS: We performed genome-wide re-annotation in Arabidopsis thaliana (Arabidopsis), Oryza sativa (rice), Capsicum annuum (pepper), Solanum tuberosum (potato), and Solanum lycopersicum (tomato) to better understand the role of PHD-finger genes in these species. Our investigation identified 875 PHD-finger genes, of which 225 (26% of total) were newly identified, including 57 (54%) novel PHD-finger genes in pepper. The PHD-finger genes of the five plant species have various integrated domains that may be responsible for the diversification of structures and functions of these genes. Evolutionary analyses suggest that PHD-finger genes were expanded recently by lineage-specific duplication, especially in pepper and potato, resulting in diverse repertoires of PHD-finger genes among the species. We validated the expression of six newly identified PHD-finger genes in pepper with qRT-PCR. Transcriptome analyses suggest potential functions of PHD-finger genes in response to various abiotic stresses in pepper. CONCLUSIONS: Our data, including the updated annotation of PHD-finger genes, provide useful information for further evolutionary and functional analyses to better understand the roles of the PHD-finger gene family in pepper.

De novo phasing resolves haplotype sequences in complex plant genomes.

Genome phasing is a recently developed assembly method that separates heterozygous eukaryotic genomic regions and builds haplotype-resolved assemblies. Because differences between haplotypes are ignored in most published de novo genomes, assemblies are available as consensus genomes consisting of haplotype mixtures, thus increasing the need for genome phasing. Here, we review the operating principles and characteristics of several freely available and widely used phasing tools (TrioCanu, FALCON-Phase, and ALLHiC). An examination of downstream analyses using haplotype-resolved genome assemblies in plants indicated significant differences among haplotypes regarding chromosomal rearrangements, sequence insertions, and expression of specific alleles that contribute to the acquisition of the biological characteristics of plant species. Finally, we suggest directions to solve addressing limitations of current genome-phasing methods. This review provides insights into the current progress, limitations, and future directions of de novo genome phasing, which will enable researchers to easily access and utilize genome-phasing in studies involving highly heterozygous complex plant genomes.

The association of obstructive sleep apnea with dyslipidemia in Korean children and adolescents: a single-center, cross-sectional study.

STUDY OBJECTIVES: To evaluate whether obstructive sleep apnea (OSA) and its severity are related to dyslipidemia and alanine transaminase elevation as a marker of nonalcoholic fatty liver disease in children. METHODS: The data collected from polysomnography, laboratory measurements (lipid profile and liver enzyme), and body mass index in children aged 0-18 years who visited the pediatric department between 2012 and 2018 were retrospectively analyzed. RESULTS: There were a total of 273 participants in the study (ages 0-6 years, 7-12 years, and 13-18 years: 61.9%, 26.4%, and 11.7%, respectively). In the ages 7-12 and 13-18 years groups, obesity was strongly associated with OSA severity (Cramer's V = 0.498, P < .001). High-density lipoprotein cholesterol levels were significantly lower in the OSA group than in the non-OSA group, irrespective of the presence of obesity. In addition, high-density lipoprotein cholesterol levels were significantly different between the OSA severity groups after adjusting for body mass index (P = .000). In participants who were obese, moderate and severe OSA were associated with alanine transaminase elevation (P = .023 and P = .045, respectively). CONCLUSIONS: This study suggests that OSA may be an independent risk factor for dyslipidemia and that OSA and obesity have a synergistic effect on alanine transaminase elevation. Early diagnosis and treatment of OSA from childhood, especially in obese children, will reduce metabolic complications. CITATION: Kang EK, Jang MJ, Kim KD, Ahn YM. The association of obstructive sleep apnea with dyslipidemia in Korean children and adolescents: a single-center, cross-sectional study. J Clin Sleep Med. 2021;17(8):1599-1605.

Mortality Rate and Major Causes of Death by Gestational Age in Korean Children under 5 Years of Age.

BACKGROUND: Preterm birth is associated with increased infant mortality. However, it is not clear whether prematurity is associated with mortality after 1 year of age. There is a lack of research on mortality rate and causes of death after infancy in preterm babies in Korea. We aimed to analyze the mortality rates and causes of deaths up to 5 years of age in Korea. METHODS: Using the Microdata Integrated Service of Statistics Korea database, this retrospective cohort study screened infants born between 2010 and 2012. After applying the exclusion criteria, 1,422,913 live births were classified into the following groups by gestational age: those born at < 32 weeks' gestation (n = 10,411), those born between 32 and 36 weeks' gestation (n = 75,657), and those born at ≥ 37 weeks' gestation (n = 1,336,845). The association of gestational age with mortality in infancy (< 1 year of age) and childhood (1-5 years of age) was analyzed, with and without covariates. The major causes of death in infancy and childhood were analyzed by gestational age. RESULTS: Overall, 4,930 (0.3%) children died between birth and 5 years of age, with 19.1% of these deaths occurring after infancy. Adjusted hazard ratios (HRs) for infant death were 78.79 (95% confidence interval [CI], 71.33-87.04) and 4.62 (95% CI, 4.07-5.24) for the < 32 and 32-36 weeks groups, respectively, compared to the full-term group; the adjusted HRs for deaths occurring at ages 1-5 years were 9.25 (95% CI, 6.85-12.50) and 2.42 (95% CI, 1.95-3.01), respectively. In infancy, conditions originating in the perinatal period were the most common cause of deaths in the < 32 and 32-36 weeks groups (88.7% and 41.9%, respectively). Contrarily, in the ≥ 37 weeks group, conditions originating in the perinatal period explained 22.7% of infant deaths, with congenital malformations primarily accounting for 29.6% of these deaths. The most common cause of death in children (after infancy) in the < 32 weeks group was perinatal causes (25.0%); in the 32-36 weeks group, congenital malformation and nervous system disease were the common causes (21.7% and 19.1%, respectively). In the ≥ 37 weeks group, injury, poisoning, and other consequences of external causes explained 26.6% of childhood deaths, followed by neoplasms and nervous system disease (15.7% and 14.7%, respectively). CONCLUSION: Low gestational age is associated with not only infant mortality but also child mortality. The major causes of death differed by gestational age in infancy and childhood. For the care of preterm infants, especially those born at < 32 weeks' gestation, particular attention and continuous monitoring are needed in consideration of the major causes of deaths until 5 years of age.

TGFam-Finder: a novel solution for target-gene family annotation in plants.

Whole-genome annotation error that omits essential protein-coding genes hinders further research. We developed Target Gene Family Finder (TGFam-Finder), an alternative tool for the structural annotation of protein-coding genes containing target domain(s) of interest in plant genomes. TGFam-Finder took considerably reduced annotation run-time and improved accuracy compared to conventional annotation tools. Large-scale re-annotation of 50 plant genomes identified an average of 150, 166 and 86 additional far-red-impaired response 1, nucleotide-binding and leucine-rich-repeat, and cytochrome P450 genes, respectively, that were missed in previous annotations. We detected significantly higher number of translated genes in the new annotations using mass spectrometry data from seven plant species compared to previous annotations. TGFam-Finder along with the new gene models can provide an optimized platform for comprehensive functional, comparative, and evolutionary studies in plants.

Positive association of breastfeeding on respiratory syncytial virus infection in hospitalized infants: a multicenter retrospective study.

BACKGROUND: Breastfeeding reportedly reduces the overall frequency of infections. Respiratory syncytial virus (RSV), the most common respiratory pathogen in infants, involves recurrent wheezing and has a pathogenic mechanism related to airway structural damage. PURPOSE: This study aimed to investigate whether breastfeeding has a beneficial effect against RSV-induced respiratory infection compared to formula feeding among infants in Korea. METHODS: We retrospectively reviewed the medical records of infants under 1 year of age who were admitted with RSV infection between January 2016 and February 2018 at the department of pediatrics of 4 hospitals. We investigated the differences in clinical parameters such as cyanosis, chest retraction, combined infection, fever duration, oxygen use, oxygen therapy duration, intensive care unit (ICU) admission, and corticosteroid treatment of exclusive breast milk feeding (BMF), artificial milk formula fed (AMF), and mixed feeding (MF) groups. RESULTS: Among the 411 infants included in our study, 94, 161, and 156 were included in the BMF, MF, and AMF groups, respectively. The rates of oxygen therapy were significantly different among the BMF (4.3%), MF (8.1%), and AMF (13.5 %) groups (P=0.042). The odds ratios (ORs) for oxygen therapy was significantly higher in the AMF group than in the BMF group (adjusted OR, 3.807; 95% confidence interval, 1.22-11.90; P=0.021). The ICU admission rate of the BMF group (1.1%) was lower than that of the MF (3.5%) and AMF (4.5%) groups; however, the dissimilarity was not statistically significant (P=0.338). CONCLUSION: The severity of RSV infection requiring oxygen therapy was lower in the BMF than the AMF group. This protective role of human milk on RSV infection might decrease the need for oxygen therapy suggesting less airway damage.

Staggered Rather Than Staged or Simultaneous Surgical Strategy May Reduce the Risk of Acute Kidney Injury in Patients Undergoing Bilateral TKA.

BACKGROUND: The strategy for bilateral total knee arthroplasty (TKA) depends on the timing of surgery for each knee. The purpose of this study was to determine whether the type of surgical strategy for bilateral TKA (staggered, staged, or simultaneous) influences the incidence of acute kidney injury (AKI) and related complications. METHODS: Enrolled patients from a single tertiary teaching hospital were divided into 3 groups according to the surgical strategy for bilateral TKA: staggered (≤7 days between the first and second procedure; n = 368), staged (8 days to 1 year between the first and second procedure; n = 265), or simultaneous (n = 820). The incidence of AKI as defined by the Kidney Disease Improving Global Outcomes (KDIGO) criteria was assessed. The rates of major postoperative complications, major adverse cardiovascular and cerebral events, intensive care unit (ICU) admissions, and mortality were also evaluated. To reduce the influence of possible confounding factors, inverse probability of treatment weighting based on propensity-score analysis was used. RESULTS: The primary outcome was the incidence of AKI according to surgical strategy. The staggered group had a lower rate of AKI compared with the other 2 groups (p < 0.001): 2.4% (9 of 368 patients), 6.0% (16 of 265), and 11.2% (92 of 820) in the staggered, staged, and simultaneous groups, respectively. CONCLUSIONS: The type of bilateral TKA strategy was an independent risk factor for the development of AKI. The assessment of additional risk factors for the development of AKI is essential before deciding on surgical strategy. LEVEL OF EVIDENCE: Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.

Predicting massive transfusion in adolescent idiopathic scoliosis patients undergoing corrective surgery: Association of preoperative radiographic findings.

Corrective surgery with a posterior approach for adolescent idiopathic scoliosis (AIS) is often accompanied by considerable bleeding. Massive transfusion after excessive hemorrhage is associated with complications such as hypothermia, coagulopathy, and acid-base imbalance. Therefore, prediction and prevention of massive transfusion are necessary to improve the clinical outcome of AIS patients. We aimed to identify the factors associated with massive transfusion in AIS patients undergoing corrective surgery. We also evaluated the clinical outcomes after massive transfusion.We included and analyzed AIS patients who underwent corrective surgery with a posterior approach from January 2008 to February 2015. We retrospectively reviewed the electronic medical records of 765 consecutive patients. We performed multivariable logistic regression analysis to assess the factors related to massive transfusion. Furthermore, we compared the effects of massive transfusion on clinical outcomes, including postoperative morbidity and hospital stay.Of 765 patients, 74 (9.7%) received massive transfusion. Body mass index (odds ratio [OR] 0.782, 95% confidence interval [CI] 0.691-0.885, P < .001) and the number of fused vertebrae (OR 1.322, 95% CI 1.027-1.703, P = .03) were associated with massive transfusion. In the comparison among the different Lenke curve types, Lenke type 4 showed the highest prevalence of massive transfusion. Patients in the massive transfusion group showed a higher incidence rate of postoperative morbidity and prolonged hospital stay.Massive transfusion was required in 9.7% of AIS patients who underwent corrective surgery with a posterior approach. A lower body mass index and higher number of fused vertebrae were associated with massive transfusion. Massive transfusion is related to poor clinical outcomes in AIS patients.