Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding.

Hybrid potato breeding will transform the crop from a clonally propagated tetraploid to a seed-reproducing diploid. Historical accumulation of deleterious mutations in potato genomes has hindered the development of elite inbred lines and hybrids. Utilizing a whole-genome phylogeny of 92 Solanaceae and its sister clade species, we employ an evolutionary strategy to identify deleterious mutations. The deep phylogeny reveals the genome-wide landscape of highly constrained sites, comprising ∼2.4% of the genome. Based on a diploid potato diversity panel, we infer 367,499 deleterious variants, of which 50% occur at non-coding and 15% at synonymous sites. Counterintuitively, diploid lines with relatively high homozygous deleterious burden can be better starting material for inbred-line development, despite showing less vigorous growth. Inclusion of inferred deleterious mutations increases genomic-prediction accuracy for yield by 24.7%. Our study generates insights into the genome-wide incidence and properties of deleterious mutations and their far-reaching consequences for breeding.

Graph pangenome captures missing heritability and empowers tomato breeding.

Missing heritability in genome-wide association studies defines a major problem in genetic analyses of complex biological traits1,2. The solution to this problem is to identify all causal genetic variants and to measure their individual contributions3,4. Here we report a graph pangenome of tomato constructed by precisely cataloguing more than 19 million variants from 838 genomes, including 32 new reference-level genome assemblies. This graph pangenome was used for genome-wide association study analyses and heritability estimation of 20,323 gene-expression and metabolite traits. The average estimated trait heritability is 0.41 compared with 0.33 when using the single linear reference genome. This 24% increase in estimated heritability is largely due to resolving incomplete linkage disequilibrium through the inclusion of additional causal structural variants identified using the graph pangenome. Moreover, by resolving allelic and locus heterogeneity, structural variants improve the power to identify genetic factors underlying agronomically important traits leading to, for example, the identification of two new genes potentially contributing to soluble solid content. The newly identified structural variants will facilitate genetic improvement of tomato through both marker-assisted selection and genomic selection. Our study advances the understanding of the heritability of complex traits and demonstrates the power of the graph pangenome in crop breeding.

Selection of allosteric dnazymes that can sense phenylalanine by expression-SELEX.

Aptamers are ligand-binding RNA or DNA molecules and have been widely examined as biosensors, diagnostic tools, and therapeutic agents. The application of aptamers as biosensors commonly requires an expression platform to produce a signal to report the aptamer-ligand binding event. Traditionally, aptamer selection and expression platform integration are two independent steps and the aptamer selection requires the immobilization of either the aptamer or the ligand. These drawbacks can be easily overcome through the selection of allosteric DNAzymes (aptazymes). Herein, we used the technique of Expression-SELEX developed in our laboratory to select for aptazymes that can be specifically activated by low concentrations of l-phenylalanine. We chose a previous DNA-cleaving DNAzyme known as II-R1 as the expression platform for its low cleavage rate and used stringent selection conditions to drive the selection of high-performance aptazyme candidates. Three aptazymes were chosen for detailed characterization and these DNAzymes were found to exhibit a dissociation constant for l-phenylalanine as low as 4.8 µM, a catalytic rate constant improvement as high as 20 000-fold in the presence of l-phenylalanine, and the ability to discriminate against closely related l-phenylalanine analogs including d-phenylalanine. This work has established the Expression-SELEX as an effective SELEX method to enrich high-quality ligand-responsive aptazymes.

Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize.

Thousands of species will be sequenced in the next few years; however, understanding how their genomes work, without an unlimited budget, requires both molecular and novel evolutionary approaches. We developed a sensitive sequence alignment pipeline to identify conserved noncoding sequences (CNSs) in the Andropogoneae tribe (multiple crop species descended from a common ancestor ∼18 million years ago). The Andropogoneae share similar physiology while being tremendously genomically diverse, harboring a broad range of ploidy levels, structural variation, and transposons. These contribute to the potential of Andropogoneae as a powerful system for studying CNSs and are factors we leverage to understand the function of maize CNSs. We found that 86% of CNSs were comprised of annotated features, including introns, UTRs, putative cis-regulatory elements, chromatin loop anchors, noncoding RNA (ncRNA) genes, and several transposable element superfamilies. CNSs were enriched in active regions of DNA replication in the early S phase of the mitotic cell cycle and showed different DNA methylation ratios compared to the genome-wide background. More than half of putative cis-regulatory sequences (identified via other methods) overlapped with CNSs detected in this study. Variants in CNSs were associated with gene expression levels, and CNS absence contributed to loss of gene expression. Furthermore, the evolution of CNSs was associated with the functional diversification of duplicated genes in the context of maize subgenomes. Our results provide a quantitative understanding of the molecular processes governing the evolution of CNSs in maize.

Improving the catalytic activity and thermostability of Aspergillus niger xylanase through computational design.

Xylanase plays the most important role in catalyzing xylan to xylose moieties. GH11 xylanases have been widely used in many fields, but most GH11 xylanases are mesophilic enzymes. To improve the catalytic activity and thermostability of Aspergillus niger xylanase (Xyn-WT), we predicted potential key mutation sites of Xyn-WT through multiple computer-aided enzyme engineering strategies. We introduce a simple and economical Ni affinity chromatography purification method to obtain high-purity xylanase and its mutants. Ten mutants (Xyn-A, Xyn-B, Xyn-C, E45T, Q93R, E45T/Q93R, A161P, Xyn-D, Xyn-E, Xyn-F) were identified. Among the ten mutants, four (Xyn-A, Xyn-C, A161P, Xyn-F) presented improved thermal stability and activity, with Xyn-F(A161P/E45T/Q93R) being the most thermally stable and active. Compared with Xyn-WT, after heat treatment at 55 °C and 60 °C for 10 min, the remaining enzyme activity of Xyn-F was 12 and 6 times greater than that of Xyn-WT, respectively, and Xyn-F was approximately 1.5 times greater than Xyn-WT when not heat treated. The pH adaptation of Xyn-F was also significantly enhanced. In summary, an improved catalytic activity and thermostability of the design variant Xyn-F has been reported.

Discovery of novel dual Bruton's tyrosine kinase (BTK) and Janus kinase 3 (JAK3) inhibitors as a promising strategy for rheumatoid arthritis.

Rheumatoid arthritis (RA) is a chronically systemic autoimmune disorder, which is related with various cellular signal pathways. Both BTK (Bruton's Tyrosine Kinase) and JAK3 (Janus Kinase 3) play important roles in the pathogenesis of rheumatoid arthritis. Herein, we reported the discovery of dual BTK/JAK3 inhibitors through bioisosterism and computer-aided drug design based on the structure of BTK inhibitor ibrutinib. We reported the discovery of dual BTK/JAK3 inhibitors which are based on the structure of BTK inhibitor ibrutinib via the method of bioisosterism and computer-aided drug design) Most of the target compounds exhibited moderate to strong inhibitory activities against BTK and JAK3. Among them, compound XL-12 stood out as the most promising candidate targeting BTK and JAK3 with potent inhibitory activities (IC50 = 2.0 nM and IC50 = 14.0 nM respectively). In the in vivo studies, compound XL-12 (40 mg/kg) exhibited more potent antiarthritic activity than ibrutinib (10 mg/kg) in adjuvant arthritis (AA) rat model. Furthermore, compound XL-12 (LD50 > 1600 mg/kg) exerted improved safety compared with ibrutinib (LD50 = 750 mg/kg). These results indicated that compound XL-12, the dual BTK/JAK3 inhibitor, might be a potent drug candidate for the treatment of RA.

Metagenomic next-generation sequencing for pulmonary infections diagnosis in patients with diabetes.

BACKGROUND: Diabetes mellitus is a major cause of high mortality and poor prognosis in patients with pulmonary infections. However, limited data on the application of metagenomic next-generation sequencing (mNGS) are available for diabetic patients. This study aimed to evaluate the diagnostic performance of mNGS in diabetic patients with pulmonary infections. METHODS: We retrospectively reviewed 184 hospitalized patients with pulmonary infections at Guizhou Provincial People's Hospital between January 2020 to October 2021. All patients were subjected to both mNGS analysis of bronchoalveolar lavage fluid (BALF) and conventional testing. Positive rate by mNGS and the consistency between mNGS and conventional testing results were evaluated for diabetic and non-diabetic patients. RESULTS: A total of 184 patients with pulmonary infections were enrolled, including 43 diabetic patients and 141 non-diabetic patients. For diabetic patients, the microbial positive rate by mNGS was significantly higher than that detected by conventional testing methods, primarily driven by bacterial detection (microbes: 95.3% vs. 67.4%, P = 0.001; bacteria: 72.1% vs. 37.2%, P = 0.001). mNGS and traditional tests had similar positive rates with regard to fungal and viral detection in diabetic patients. Klebsiella pneumoniae was the most common pathogen identified by mNGS in patients with diabetes. Moreover, mNGS identified pathogens in 92.9% (13/14) of diabetic patients who were reported negative by conventional testing. No significant difference was found in the consistency of the two tests between diabetic and non-diabetic groups. CONCLUSIONS: mNGS is superior to conventional microbiological tests for bacterial detection in diabetic patients with pulmonary infections. mNGS is a valuable tool for etiological diagnosis of pulmonary infections in diabetic patients.

The structural and molecular mechanisms of type II PETases: a mini review.

The advent of plastics has led to significant advances for humans, although the accompanying pollution has also been a source of concern for countries globally. Consequently, a biological method to effectively degrade polyethylene terephthalate (PET) has been an area of significant scientific interest. Following the report of the highly efficient PET hydrolase from the bacterium Ideonella sakaiensis strain 201-F6 (i.e., IsPETase) in 2016, its structure has been extensively studied, showing that it belongs to the type II PETase group. Unlike type I PETases that include most known cutinases, structural investigations of type II PETases have only been conducted since 2017. Type II PETases are further divided into type IIa and IIb enzymes. Moreover, even less research has been conducted on type IIa plastic-degrading enzymes. Here, we present a review of recent studies of the structure and mechanism of type II PETases, using the known structure of the type IIa PETase PE-H from the marine bacterium Pseudomonas aestusnigri in addition to the type IIb enzyme IsPETase as representatives. These studies have provided new insights into the structural features of type II PETases that exhibit PET catalytic activity. In addition, recent studies investigating the rational design of IsPETases are reviewed and summarized alongside a discussion of controversies surrounding PETase investigations.

Genome-wide association study of eigenvectors provides genetic insights into selective breeding for tomato metabolites.

BACKGROUND: Long-term domestication and intensive breeding of crop plants aim to establish traits desirable for human needs, and characteristics related to yield, disease resistance, and postharvest storage have traditionally received considerable attention. These processes have led also to negative consequences, as is the case of loss of variants controlling fruit quality, for instance in tomato. Tomato fruit quality is directly associated to metabolite content profiles; however, a full understanding of the genetics affecting metabolite content during tomato domestication and improvement has not been reached due to limitations of the single detection methods previously employed. Here, we aim to reach a broad understanding of changes in metabolite content using a genome-wide association study (GWAS) with eigenvector decomposition (EigenGWAS) on tomato accessions. RESULTS: An EigenGWAS was performed on 331 tomato accessions using the first eigenvector generated from the genomic data as a "phenotype" to understand the changes in fruit metabolite content during breeding. Two independent gene sets were identified that affected fruit metabolites during domestication and improvement in consumer-preferred tomatoes. Furthermore, 57 candidate genes related to polyphenol and polyamine biosynthesis were discovered, and a major candidate gene chlorogenate: glucarate caffeoyltransferase (SlCGT) was identified, which affected the quality and diseases resistance of tomato fruit, revealing the domestication mechanism of polyphenols. CONCLUSIONS: We identified gene sets that contributed to consumer liking during domestication and improvement of tomato. Our study reports novel evidence of selective sweeps and key metabolites controlled by multiple genes, increasing our understanding of the mechanisms of metabolites variation during those processes. It also supports a polygenic selection model for the application of tomato breeding.

The application of riboswitch sequencing for human gut bacterial classification and identification.

Bacteria, especially gut bacteria play important roles in human health and diseases. The classification of many bacterial genera by the 16S ribosomal RNA (rRNA) has failed due to its low inter-species resolution. Given the wide distribution of riboswitches in bacteria, they may help 16S rRNA differentiate closely related species. We found that among 28 groups of species that could not be distinguished by 16S rRNA, eight of them could be separated by the TPP riboswitch and other riboswitches. Moreover, the species in the 16S rRNA database and these riboswitch databases overlap, therefore, using riboswitch databases can help 16S rRNA better identify species. In addition, we used Klenow DNA polymerase and a pair of short primers to facilitate the library construction of TPP riboswitches for sequencing. The sequencing results showed that the TPP riboswitch could detect the major phyla similar to those detected by 16S rRNA. Therefore, the TPP riboswitch and other riboswitch classes could potentially be applied to gut bacteria classification.

Simultaneous accumulation of astaxanthin and ß-carotene in Chlamydomonas reinhardtii by the introduction of foreign ß-carotene hydroxylase gene in response to high light stress.

Carotenoids are important photosynthetic pigments with many physiological functions, nutritional properties and high commercial value. ß-carotene hydroxylase is one of the key enzymes in the carotenoid synthesis pathway of Chlamydomonas reinhardtii for the conversion of ß-carotene to astaxanthin. The vector p64DZ containing the ß-carotene hydroxylase gene crtZ from Haematococcus pluvialis was transformed into C. reinhardtii CC-503. The transformants were selected by alternate culture in solid-liquid medium containing spectinomycin (100 µg mL-1). PCR results indicated that the gene crtZ and aadA were integrated into the genome of C. reinhardtii. RT-PCR analysis showed that the gene crtZ was transcribed in Chlamydomonas transformants. HPLC analysis showed that the content of astaxanthin and ß-carotene in cells of C. reinhardtii were simultaneously increased. Under medium light intensity cultivation (60 µmol m-2 s-1), transgenic C. reinhardtii had an 85.8% increase in ß-carotene content compared with the wild type. The content of astaxanthin and ß-carotene reached 1.97 ± 0.13 mg g-1 fresh cell weight (FCW) and 105.94 ± 5.84 µg g-1 FCW, which were increased 18% and 42.4% than the wild type after 6 h of high light treatment (200 µmol m-2 s-1), respectively. Our results indicate the regulatory effect on pigments in C. reinhardtii by ß-carotene hydroxylase gene of H. pluvialis, and demonstrate the positive effect of high light stress on pigment accumulation in transgenic C. reinhardtii.

Transfer of Invitro CD4 + T Cells with Hypomethylation of Perforin Promoter into Rats' Abdomens Causes Autoimmune Emphysema.

Our previous study suggested that hypomethylation of perforin promoter of CD4 + T cells might be involved in the pathogenesis of autoimmune emphysema of rats. Whether transfer of this kind of cells hypomethylated in vitro into naive immunocompetent rats also results in emphysema is unknown yet. To test the hypothesis above, thirty Sprague Dawley (SD) rats were randomly divided into three groups: a model group (n = 10), a normal control group (n = 10) and a sham operation group (n = 10). In the model group, spleen-derived CD4 + T cells of normal rats were treated with 5-azacytidine (5-Aza), complete Freund's adjuvant and Phosphate Buffered Saline (PBS), then transferred into naive immunocompetent rats. The normal control group was injected with CD4 + T lymphocytes from spleens of normal rats and the same amount of adjuvant and PBS as above. In sham operation group, normal rats were injected intraperitoneally with complete Freund's adjuvant and PBS. Histopathological evaluations (mean linear Intercept (MLI) and mean alveolar numbers (MAN)), anti-endothelial cell antibodies (AECA) in serum and bronchoalveolar lavage fluid (BALF), lung vascular endothelial growth factor (VEGF)), the apoptotic index (AI) of alveolar septal cells and the methylation levels of perforin promoter of CD4 + T cells were investigated. The levels of the methylation above and MAN were lower in the model group than in the control and the sham operation group, while the AECA in serum and BALF, VEGF, MLI and the AI were greater (all p < 0.05). The methylation levels of perforin promoter were positively correlated with the MAN (r = 0.747, p < 0.05) and negatively correlated with AI, AECA, MLI, and VEGF (r was -0.789, -0.746, -0.743, -0.660, respectively, all p < 0.05). This study suggests that transfer of invitro CD4 + T cells with hypomethylation of perforin promoter into rats causes autoimmune emphysema, possibly by increasing expression of VEGF and promoting alveolar septal cell apoptosis.

Identification of 11 candidate structured noncoding RNA motifs in humans by comparative genomics.

BACKGROUND: Only 1.5% of the human genome encodes proteins, while large part of the remaining encodes noncoding RNAs (ncRNA). Many ncRNAs form structures and perform many important functions. Accurately identifying structured ncRNAs in the human genome and discovering their biological functions remain a major challenge. RESULTS: Here, we have established a pipeline (CM-line) with the following features for analyzing the large genomes of humans and other animals. First, we selected species with larger genetic distances to facilitate the discovery of covariations and compatible mutations. Second, we used CMfinder, which can generate useful alignments even with low sequence conservation. Third, we removed repetitive sequences and known structured ncRNAs to reduce the workload of CMfinder. Fourth, we used Infernal to find more representatives and refine the structure. We reported 11 classes of structured ncRNA candidates with significant covariations in humans. Functional analysis showed that these ncRNAs may have variable functions. Some may regulate circadian clock genes through poly (A) signals (PAS); some may regulate the elongation factor (EEF1A) and the T-cell receptor signaling pathway by cooperating with RNA binding proteins. CONCLUSIONS: By searching for important features of RNA structure from large genomes, the CM-line has revealed the existence of a variety of novel structured ncRNAs. Functional analysis suggests that some newly discovered ncRNA motifs may have biological functions. The pipeline we have established for the discovery of structured ncRNAs and the identification of their functions can also be applied to analyze other large genomes.

Low-threshold upconverted single-mode lasing from CdS hexagonal microcavities.

Upconversion micro/nanolasers are promising in fundamental physics research and practical applications. However, due to the limitation of gain medium and cavity quality, such lasers still suffer from a high lasing threshold (P th). Herein, upconverted whispering-gallery-mode lasing by two-photon absorption is achieved from CdS microplatelets with single-mode emission and low threshold (∼1.2 mJ cm-2). The threshold is three times lower than the best reported value in previous CdS upconversion lasers. Moreover, wavelength-tunable upconverted single-mode lasing is demonstrated from 510.4 to 518.9 nm with narrow linewidths around 0.85 nm, which is further verified through numerical simulations. In addition, the size-dependent lasing behavior is realized from single-mode to multimode oscillation; the corresponding lasing threshold decreases with increasing cavity edge length (L), following a P th ∝ 1/L 2 relationship. These results underscore the promise of CdS microplatelets for developing chip-level frequency upconversion lasers.

Enzymatic activity of palmitoyl-protein thioesterase-1 in serum from schizophrenia significantly associates with schizophrenia diagnosis scales.

Genome-wide association studies have confirmed that schizophrenia is an inheritable multiple-gene mental disorder. Longitudinal studies about depression, first episode psychosis (FEP) and acute psychotic relapse have mostly searched for brain imaging biomarkers and inflammatory markers from the blood. However, to the best of our knowledge, the association between enzymatic activities with diagnosis or prediction of treatment response in people with schizophrenia has barely been validated. Under the Longitudinal Study of National Mental Health Work Plan (2015-2020), we have studied a subsample of approximately 36 individuals from the cohort with data on palmitoyl-protein thioesterase-1 enzymatic activity from FEP and performed a bivariate correlation analysis with psychiatric assessment scores. After adjusting for sex, age, body mass index (BMI) and total serum protein, our data demonstrated that PPT1 enzymatic activity is significantly associated with schizophrenia and its Positive and Negative Syndrome Scale (PANSS) scores. This longitudinal study compared the PPT1 enzymatic activity in FEP schizophrenia patients and healthy volunteers, and the former exhibited a significant 1.5-fold increase in PPT1 enzymatic levels (1.79 mmol/L/h/mL, and 1.18 mmol/L/h/mL; P < 0.05; 95% CI, 2.3-2.9 and 1.4-1.8). The higher PPT1 enzymatic levels in FEP schizophrenia patients were positively associated with larger PANSS scaling scores (r = 0.32, P = 0.0079 for positive scaling; r = 0.41, P = 0.0006 for negative scaling; r = 0.45, P = 0.0001 for general scaling; and r = 0.34, P = 0.0048 for PNASS-S scaling). Higher enzymatic PPT1 in FEP schizophrenia patients is significantly associated with increased PANSS scaling values, indicating more serious rates of developing psychosis. Enzymatic activity of PPT1 may provide an important new view for schizophrenia disorders.

Domain-functional analyses of PIWIL1 and PABPC1 indicate their synergistic roles in protein translation via 3'-UTRs of meiotic mRNAs.

Translational regulation plays a central role during post-meiotic development of male germ cells. Previous studies suggested that P-element induced wimpy testis like 1 (PIWIL1), a PIWI-interacting RNA (piRNA) binding protein that is critical for sperm development, participates in the maintenance and translational regulation of post-meiotic mRNAs in haploid spermatids. However, how PIWIL1 regulates protein translation remains largely unclear. Using biochemical assays, we show here that PIWIL1 utilizes different domains to interact with post-meiotic mRNAs and Poly-A binding protein cytoplasmic 1 (PABPC1), a general protein translation regulator. PIWIL1 binds 3'-untranslated regions (3'-UTRs) of several spermiogenic mRNAs via its N-terminal domain, whereas its interactions with PABPC1 are mediated through its N- and C-terminal domains in an RNA-dependent manner. Using a heterologous cell system, we analyzed its effects on protein translation via luciferase reporter assay and sucrose gradient sedimentation. It was found that PIWIL1 augments protein translation with PABPC1 in the presence of 3'-UTRs of post-meiotic mRNAs. While both the N-terminal RNA recognition motif (RRM) domain and the central linker region of PABPC1 stimulate translation, only the PIWI Argonaute and Zwille (PAZ) domain of PIWIL1 positively affects translation of reporter mRNAs. Interestingly, the PAZ domain was found absent from polysomal fractions, in contrast to the N- and C-terminal domains of PIWIL1. Taken together, the results suggest that PIWIL1 interacts with various partners using different domains and participates in translational regulation partly through 3'-UTRs. It will be of interest to further explore how PIWIL1 elicit its versatile functions, including translational regulation of post-meiotic mRNAs through intrinsic structural changes and extrinsic signals during mouse spermiogenesis under more physiological settings.

Complex genetic architecture underlies maize tassel domestication.

Maize (Zea mays) tassels underwent profound morphological changes during maize domestication and improvement. Although a number of genes affecting maize inflorescence development have been identified, the genetic basis of the morphological changes in maize tassels since domestication is not well understood. Here, using a large population of 866 maize-teosinte BC2 S3 recombinant inbred lines genotyped using 19 838 single nucleotide polymorphism (SNP) markers, we performed high-resolution quantitative trait locus (QTL) mapping for five tassel morphological traits. We showed that the five tassel traits were associated with different genetic architecture features. Known genes for maize inflorescence development identified by mutagenesis were significantly enriched in the tassel trait QTLs, and many of these genes, including ramosa1 (ra1), barren inflorescence2 (bif2), unbranched2 (ub2), zea floricaula leafy2 (zfl2) and barren stalk fastigiate1 (baf1), showed evidence of selection. An in-depth nucleotide diversity analysis at the bif2 locus identified strong selection signatures in the 5'-regulatory region. We also found that several known flowering time genes co-localized with tassel trait QTLs. A further association analysis indicated that the maize photoperiod gene ZmCCT was significantly associated with tassel size variation. Using near-isogenic lines, we narrowed down a major-effect QTL for tassel length, qTL9-1, to a 513-kb physical region. These results provide important insights into the genetic architecture that controls maize tassel evolution.

The genetic architecture of leaf number and its genetic relationship to flowering time in maize.

The number of leaves and their distributions on plants are critical factors determining plant architecture in maize (Zea mays), and leaf number is frequently used as a measure of flowering time, a trait that is key to local environmental adaptation. Here, using a large set of 866 maize-teosinte BC2 S3 recombinant inbred lines genotyped by using 19,838 single nucleotide polymorphism markers, we conducted a comprehensive genetic dissection to assess the genetic architecture of leaf number and its genetic relationship to flowering time. We demonstrated that the two components of total leaf number, the number of leaves above (LA) and below (LB) the primary ear, were under relatively independent genetic control and might be subject to differential directional selection during maize domestication and improvement. Furthermore, we revealed that flowering time and leaf number are commonly regulated at a moderate level. The pleiotropy of the genes ZCN8, dlf1 and ZmCCT on leaf number and flowering time were validated by near-isogenic line analysis. Through fine mapping, qLA1-1, a major-effect locus that specifically affects LA, was delimited to a region with severe recombination suppression derived from teosinte. This study provides important insights into the genetic basis of traits affecting plant architecture and adaptation. The genetic independence of LA from LB enables the optimization of leaf number for ideal plant architecture breeding in maize.

AKAP3 synthesis is mediated by RNA binding proteins and PKA signaling during mouse spermiogenesis.

Mammalian spermatogenesis is regulated by coordinated gene expression in a spatiotemporal manner. The spatiotemporal regulation of major sperm proteins plays important roles during normal development of the male gamete, of which the underlying molecular mechanisms are poorly understood. A-kinase anchoring protein 3 (AKAP3) is one of the major components of the fibrous sheath of the sperm tail that is formed during spermiogenesis. In the present study, we analyzed the expression of sperm-specific Akap3 and the potential regulatory factors of its protein synthesis during mouse spermiogenesis. Results showed that the transcription of Akap3 precedes its protein synthesis by about 2 wk. Nascent AKAP3 was found to form protein complex with PKA and RNA binding proteins (RBPs), including PIWIL1, PABPC1, and NONO, as revealed by coimmunoprecipitation and protein mass spectrometry. RNA electrophoretic gel mobility shift assay showed that these RBPs bind sperm-specific mRNAs, of which proteins are synthesized during the elongating stage of spermiogenesis. Biochemical and cell biological experiments demonstrated that PIWIL1, PABPC1, and NONO interact with each other and colocalize in spermatids' RNA granule, the chromatoid body. In addition, NONO was found in extracytoplasmic granules in round spermatids, whereas PIWIL1 and PABPC1 were diffusely localized in cytoplasm of elongating spermatids, indicating their participation at different steps of mRNA metabolism during spermatogenesis. Interestingly, type I PKA subunits colocalize with PIWIL1 and PABPC1 in the cytoplasm of elongating spermatids and cosediment with the RBPs in polysomal fractions on sucrose gradients. Further biochemical analyses revealed that activation of PKA positively regulates AKAP3 protein synthesis without changing its mRNA level in elongating spermatids. Taken together, these results indicate that PKA signaling directly participates in the regulation of protein translation in postmeiotic male germ cells, underscoring molecular mechanisms that regulate protein synthesis during mouse spermiogenesis.

Enhanced ammonia oxidation by a photoelectrocatalysis­chlorine system: The role of ClO• and free chlorine.

The decomposition of ammonia-N to environmental-friendly N2 remains a fundamental problem for water treatment. We proposed a way to selectively and efficiently oxidize ammonia to N2 through an integrated photoeletrocatalysis­chlorine reactions (PECCl) system based on a bifunctional TiO2 nanotube photoanode. The ·OH and HClO can be simultaneously generated on the TiO2 nanotube photoanode in this system, which can in situ form ClO· for efficient ammonia removal. Compared with electrochemical­chlorine (EC-Cl), photocatalysis­chlorine (PC-Cl) and photoelectrocatalysis (PEC) systems, the PEC-Cl system exhibited much higher electrocatalytic activity due to the synergetic effect of photoelectrocatalyst and electrocatalyst in bifunctional TiO2 nanotube electrode. The removal efficiency of ammonia-N and total-N reached 100.0 % and 93.3 % at 0.3 V (vs Ag/AgCl) in the PEC-Cl system. Moreover, the system was efficient under various pH conditions. The reactions between ClO-/ClO· and the N-containing intermediates contributed to the high performance of the system, which expanded the reactions from the electrode surface to the electrolyte. Furthermore, radical scavenging and free chlorine determination experiments confirmed that ClO· and free chlorine were the main active species that enabled the ammonia oxidation. This study presents new understanding on the role of active species for ammonia removal in wastewater.