RNA methylation influences TDP43 binding and disease pathogenesis in models of amyotrophic lateral sclerosis and frontotemporal dementia.

RNA methylation at adenosine N6 (m6A) is one of the most common RNA modifications, impacting RNA stability, transport, and translation. Previous studies uncovered RNA destabilization in amyotrophic lateral sclerosis (ALS) models in association with accumulation of the RNA-binding protein TDP43. Here, we show that TDP43 recognizes m6A RNA and that RNA methylation is critical for both TDP43 binding and autoregulation. We also observed extensive RNA hypermethylation in ALS spinal cord, corresponding to methylated TDP43 substrates. Emphasizing the importance of m6A for TDP43 binding and function, we identified several m6A factors that enhance or suppress TDP43-mediated toxicity via single-cell CRISPR-Cas9 in primary neurons. The most promising modifier-the canonical m6A reader YTHDF2-accumulated within ALS spinal neurons, and its knockdown prolonged the survival of human neurons carrying ALS-associated mutations. Collectively, these data show that m6A modifications modulate RNA binding by TDP43 and that m6A is pivotal for TDP43-related neurodegeneration in ALS.

The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize.

Autocrine signaling pathways regulated by RAPID ALKALINIZATION FACTORs (RALFs) control cell wall integrity during pollen tube germination and growth in Arabidopsis (Arabidopsis thaliana). To investigate the role of pollen-specific RALFs in another plant species, we combined gene expression data with phylogenetic and biochemical studies to identify candidate orthologs in maize (Zea mays). We show that Clade IB ZmRALF2/3 mutations, but not Clade III ZmRALF1/5 mutations, cause cell wall instability in the sub-apical region of the growing pollen tube. ZmRALF2/3 are mainly located in the cell wall and are partially able to complement the pollen germination defect of their Arabidopsis orthologs AtRALF4/19. Mutations in ZmRALF2/3 compromise pectin distribution patterns leading to altered cell wall organization and thickness culminating in pollen tube burst. Clade IB, but not Clade III ZmRALFs, strongly interact as ligands with the pollen-specific Catharanthus roseus RLK1-like (CrRLK1L) receptor kinases Z. mays FERONIA-like (ZmFERL) 4/7/9, LORELEI-like glycosylphosphatidylinositol-anchor (LLG) proteins Z. mays LLG 1 and 2 (ZmLLG1/2), and Z. mays pollen extension-like (PEX) cell wall proteins ZmPEX2/4. Notably, ZmFERL4 outcompetes ZmLLG2 and ZmPEX2 outcompetes ZmFERL4 for ZmRALF2 binding. Based on these data, we suggest that Clade IB RALFs act in a dual role as cell wall components and extracellular sensors to regulate cell wall integrity and thickness during pollen tube growth in maize and probably other plants.

Neuronal activity regulates Matrin 3 abundance and function in a calcium-dependent manner through calpain-mediated cleavage and calmodulin binding.

RNA-binding protein (RBP) dysfunction is a fundamental hallmark of amyotrophic lateral sclerosis (ALS) and related neuromuscular disorders. Abnormal neuronal excitability is also a conserved feature in ALS patients and disease models, yet little is known about how activity-dependent processes regulate RBP levels and functions. Mutations in the gene encoding the RBP Matrin 3 (MATR3) cause familial disease, and MATR3 pathology has also been observed in sporadic ALS, suggesting a key role for MATR3 in disease pathogenesis. Here, we show that glutamatergic activity drives MATR3 degradation through an NMDA receptor-, Ca2+-, and calpain-dependent mechanism. The most common pathogenic MATR3 mutation renders it resistant to calpain degradation, suggesting a link between activity-dependent MATR3 regulation and disease. We also demonstrate that Ca2+ regulates MATR3 through a nondegradative process involving the binding of Ca2+/calmodulin to MATR3 and inhibition of its RNA-binding ability. These findings indicate that neuronal activity impacts both the abundance and function of MATR3, underscoring the effect of activity on RBPs and providing a foundation for further study of Ca2+-coupled regulation of RBPs implicated in ALS and related neurological diseases.

Heat stress at the bicellular stage inhibits sperm cell development and transport into pollen tubes.

For successful double fertilization in flowering plants (angiosperms), pollen tubes deliver 2 nonmotile sperm cells toward female gametes (egg and central cell, respectively). Heatwaves, especially during the reproduction period, threaten male gametophyte (pollen) development, resulting in severe yield losses. Using maize (Zea mays) as a crop and grass model system, we found strong seed set reduction when moderate heat stress was applied for 2 d during the uni- and bicellular stages of pollen development. We show that heat stress accelerates pollen development and impairs pollen germination capabilities when applied at the unicellular stage. Heat stress at the bicellular stage impairs sperm cell development and transport into pollen tubes. To understand the course of the latter defects, we used marker lines and analyzed the transcriptomes of isolated sperm cells. Heat stress affected the expression of genes associated with transcription, RNA processing and translation, DNA replication, and the cell cycle. This included the genes encoding centromeric histone 3 (CENH3) and α-tubulin. Most genes that were misregulated encode proteins involved in the transition from metaphase to anaphase during pollen mitosis II. Heat stress also activated spindle assembly check point and meta- to anaphase transition genes in sperm cells. In summary, misregulation of the identified genes during heat stress at the bicellular stage results in sperm cell development and transport defects ultimately leading to sterility.

Disrupting the Balance of Protein Quality Control Protein UBQLN2 Accelerates Tau Proteinopathy.

Tau protein accumulation drives toxicity in several neurodegenerative disorders. To better understand the pathways regulating tau homeostasis in disease, we investigated the role of ubiquilins (UBQLNs)-a class of proteins linked to ubiquitin-mediated protein quality control (PQC) and various neurodegenerative diseases-in regulating tau. Cell-based assays identified UBQLN2 as the primary brain-expressed UBQLN to regulate tau. UBQLN2 efficiently lowered wild-type tau levels regardless of aggregation, suggesting that UBQLN2 interacts with and regulates tau protein under normal conditions or early in disease. Moreover, UBQLN2 itself proved to be prone to accumulation as insoluble protein in male and female tau transgenic mice and the human tauopathy progressive supranuclear palsy. Genetic manipulation of UBQLN2 in a tauopathy mouse model demonstrated that a physiological UBQLN2 balance is required for tau homeostasis. UBQLN2 overexpression exacerbated phosphorylated tau pathology and toxicity in mice expressing P301S mutant tau, whereas P301S mice lacking UBQLN2 showed significantly reduced phosphorylated tau. Further studies support the view that an imbalance of UBQLN2 perturbs ubiquitin-dependent PQC and autophagy. We conclude that changes in UBQLN2 levels, whether because of pathogenic mutations or secondary to disease states, such as tauopathy, contribute to proteostatic imbalances that exacerbate neurodegeneration.SIGNIFICANCE STATEMENT We defined a role for the protein quality control protein Ubiquilin-2 (UBQLN2), in age-related neurodegenerative tauopathies. This group of disorders is characterized by the accumulation of tau protein aggregates, which differ when UBQLN2 levels are altered. Given the lack of effective disease-modifying therapies for tauopathies and the function of UBQLN2 in handling various disease-linked proteins, we explored the role of UBQLN2 in regulating tau. We found that UBQLN2 reduced tau levels in cell models but behaved differently in mouse brain, where it accelerated mutant tau pathology and tau-mediated toxicity. A better understanding of the diverse functions of regulatory proteins like UBQLN2 can elucidate some of the causative factors in neurodegenerative disease and outline new routes to therapeutic intervention.

Initial treatment with a single capsule containing half-dose quadruple therapy vs standard-dose dual therapy in hypertensive patients (QUADUAL): Study protocol for a randomized, blinded, crossover trial.

BACKGROUND: Combined antihypertensive therapy has obvious advantages over single drug therapy. Hypertension guidelines fully affirm the efficacy of dual combination in initial antihypertensive therapy. Recent studies have also pointed out that the quadruple combination of very low-dose antihypertensive drugs is superior to single drugs. However, whether low-dose quadruple therapy is better than dual combination is unknown. OBJECTIVE: To evaluate and compare the efficacy and safety of half-dose quadruple therapy vs standard-dose dual therapy in the initial treatment of hypertensive patients with systolic/diastolic blood pressure 140-179/90-109 mm Hg. METHODS: A randomized double-blind crossover clinical trial will be conducted to compare the efficacy and safety of low-dose quadruple antihypertensives (irbesartan 75 mg + metoprolol 23.75 mg + amlodipine 2.5 mg + indapamide 1.25 mg) with standard-dose dual antihypertensives (irbesartan 150 mg + amlodipine 5 mg) in the initial treatment of patients with mild to moderate hypertension (140-179/90-109 mm Hg). Ninety patients are required and will be recruited and randomly assigned in a 1:1 ratio to 2 crossover groups. Two groups will receive a different combination therapy for 4 weeks, then switch to the other combination therapy for 4 weeks, with a 2-week wash-out. The patients will be followed up for 4 weeks to compare the antihypertensive effects and related adverse effects of the 2 antihypertensive combination treatments. CONCLUSIONS: We present the rationale for the design of the QUADUAL trial. The trial started in July 2022 and is expected to be completed by August 2023. The study aims to evaluate if an initial treatment regimen of quadruple combination of half-dose blood pressure medications will result in greater reduction in blood pressure and fewer side effects compared to standard dose dual therapy. REGISTRATION: www. CLINICALTRIALS: gov (NCT05377203).

Effects of different sleep disorders on frailty in the elderly: a systematic review and meta-analysis of observational studies.

STUDY OBJECTIVES: Frailty is frequently reported following sleep disorders; however, the extent to which sleep disorders influence frailty remains unclear. In the current study, we performed a meta-analysis to evaluate the quantitative effects of different sleep disorders on frailty in the elderly. METHODS: We conducted a systematic search of several databases, including PubMed, Web of Science, Embase, and Scopus, to retrieve articles published from May 2009 to June 2021. The data outcomes are expressed as the odds ratio (OR) and 95% confidence interval (CI). RESULTS: Eighteen studies were included, with 39669 participants. Older adults with sleep disorders were found to have a higher risk of frailty (pooled OR = 1.49, 95%CI = 1.35-1.64, p < 0.01). Specifically, daytime sleepiness (pooled OR = 1.69, 95%CI = 1.09-2.61, p < 0.01), short sleep duration (pooled OR = 1.36, 95%CI = 1.20-1.54, p = 0.45), long sleep duration (pooled OR = 1.99, 95%CI = 1.39-2.85, p = 0.02), sleep latency extension (pooled OR = 1.38, 95%CI = 1.19-1.60, p = 0.72), and sleep disordered breathing (pooled OR = 1.30, 95%CI = 1.11-1.53, p = 0.37) were correlated with frailty. CONCLUSIONS: The risk of frailty differs between older adults with sleep disorders and controls, suggesting that the relationships between different sleep disorders and frailty vary. These results highlight the need to monitor sleep disorders of the elderly and conduct intervention to prevent or delay the frailty process.

Environmental noise exposure and health outcomes: an umbrella review of systematic reviews and meta-analysis.

BACKGROUND: Environmental noise is becoming increasingly recognized as an urgent public health problem, but the quality of current studies needs to be assessed. To evaluate the significance, validity and potential biases of the associations between environmental noise exposure and health outcomes. METHODS: We conducted an umbrella review of the evidence across meta-analyses of environmental noise exposure and any health outcomes. A systematic search was done until November 2021. PubMed, Cochrane, Scopus, Web of Science, Embase and references of eligible studies were searched. Quality was assessed by AMSTAR and Grading of Recommendations, Assessment, Development and Evaluation (GRADE). RESULTS: Of the 31 unique health outcomes identified in 23 systematic reviews and meta-analyses, environmental noise exposure was more likely to result in a series of adverse outcomes. Five percent were moderate in methodology quality, the rest were low to very low and the majority of GRADE evidence was graded as low or even lower. The group with occupational noise exposure had the largest risk increment of speech frequency [relative risk (RR): 6.68; 95% confidence interval (CI): 3.41-13.07] and high-frequency (RR: 4.46; 95% CI: 2.80-7.11) noise-induced hearing loss. High noise exposure from different sources was associated with an increased risk of cardiovascular disease (34%) and its mortality (12%), elevated blood pressure (58-72%), diabetes (23%) and adverse reproductive outcomes (22-43%). In addition, the dose-response relationship revealed that the risk of diabetes, ischemic heart disease (IHD), cardiovascular (CV) mortality, stroke, anxiety and depression increases with increasing noise exposure. CONCLUSIONS: Adverse associations were found for CV disease and mortality, diabetes, hearing impairment, neurological disorders and adverse reproductive outcomes with environmental noise exposure in humans, especially occupational noise. The studies mostly showed low quality and more high-quality longitudinal study designs are needed for further validation in the future.

Dissipation-Induced Information Scrambling in a Collision Model.

In this paper, we present a collision model to stroboscopically simulate the dynamics of information in dissipative systems. In particular, an all-optical scheme is proposed to investigate the information scrambling of bosonic systems with Gaussian environmental states. Varying the states of environments, in the presence of dissipation, transient tripartite mutual information of system modes may show negative value, signaling the appearance of information scrambling. We also find that dynamical indivisibility based non-Markovianity plays dual roles in affecting the dynamics of information.

Modification of the effects of nitrogen dioxide and sulfur dioxide on congenital limb defects by meteorological conditions.

STUDY QUESTION: Can meteorological conditions modify the associations between NO2 and SO2 exposure and congenital limb defects (CLDs) during the first trimester of pregnancy? SUMMARY ANSWER: Increases in NO2 and SO2 exposure were consistently associated with higher risks of CLDs during the first trimester of pregnancy; both low- and high-temperature exposure and high air humidity act synergistically with the two air pollutants on CLDs. WHAT IS KNOWN ALREADY: Animal studies have indicated air pollutants are associated with CLDs, but corresponding epidemiological studies are limited with equivocal conclusions. Meteorological conditions are closely connected to the generation, diffusion, distribution and even chemical toxicity of air pollutants. STUDY DESIGN, SIZE, DURATION: This case-control study included 972 cases of CLDs and 9720 controls in Changsha, China during 2015-2018. PARTICIPANTS/MATERIALS, SETTING, METHODS: Cases from the hospital based monitoring system for birth defects (including polydactyly, syndactyly, limb shortening, and clubfoot) and healthy controls from the electronic medical records system were studied. Complete data on daily average NO2 and SO2 concentrations and meteorological variables were obtained from local monitoring stations to estimate monthly individual exposures during the first trimester of pregnancy, using the nearest monitoring station approach for NO2 and SO2 concentrations, and the city-wide average approach for temperature and relative humidity, respectively. The 25th and 75th percentiles of daily mean temperature, as well as the 50th percentile of daily mean relative humidity during the study period were used to classify high- and low-temperature exposure, and high humidity exposure based on existing evidence and local climate characteristics. Multivariate logistic regression models were used to estimate the independent effects per 10 µg/m3 increase in NO2 and SO2 on CLDs, and the attribute proportions of interaction (API) were used to quantify the additive joint effects of air pollutants with meteorological conditions after including a cross product interaction term in the regression models. MAIN RESULTS AND THE ROLE OF CHANCE: NO2 and SO2 exposures during the first trimester of pregnancy were consistently and positively associated with overall CLDs and subtypes, with adjusted odd ratios (aORs) ranging from 1.13 to 1.27 for NO2, and from 1.37 to 2.49 for SO2. The effect estimates were generally observed to be the strongest in the first month and then attenuated in the second and third months of pregnancy. Synergistic effects of both low and high temperature in combination with NO2 (with APIs ranging from 0.07 to 0.38) and SO2 (with APIs ranging from 0.18 to 0.51) appeared in the first trimester of pregnancy. Several significant modifying effects by high humidity were also observed, especially for SO2 (with APIs ranging from 0.13 to 0.38). Neither NO2 nor SO2 showed an interactive effect with season of conception. LIMITATIONS, REASONS FOR CAUTION: The methods used to estimate individual exposure levels of air pollutants and meteorological factors may lead to the misclassification bias because of the lack of information on maternal activity patterns and residential mobility during pregnancy. Moreover, we were unable to consider several potentially confounding factors, including socioeconomic status, maternal nutrient levels, alcohol use and smoking during early pregnancy due to unavailable data, although previous studies have suggested limited change to the results after when including these factors in the analysis. WIDER IMPLICATIONS OF THE FINDINGS: The findings are helpful for understanding the combined effects of air pollution and meteorological conditions on birth defects. Environmental policies and practices should be formulated and implemented to decrease air pollutant emissions and improve meteorological conditions to reduce their harmful effects on pregnancy. Additionally, pregnant women should be suggested to reduce outdoor time when the air quality is poor, especially when ambient temperature is higher or lower than what is comfortable, or when it is excessively humid. STUDY FUNDING/COMPETING INTEREST(S): The study is funded by Major Scientific and Technological Projects for Collaborative Prevention and Control of Birth Defects in Hunan Province (2019SK1012), Major Research and Development Projects in Hunan Province (2018SK2060) and Scientific and Technological Department Projects in Hunan Province (2017SK50802). There are no competing interests. TRIAL REGISTRATION NUMBER: N/A.

First trimester exposure to ambient gaseous air pollutants and risk of orofacial clefts: a case-control study in Changsha, China.

BACKGROUND: A growing body of studies have investigated the association between air pollution exposure during early pregnancy and the risk of orofacial clefts, but these studies put more emphasis on particulate matter and reported inconsistent results, while research on the independent effects of gaseous air pollutants on orofacial clefts has been quite inadequate, especially in China. METHODS: A case-control study was conducted in Changsha, China from 2015 to 2018. A total of 446 cases and 4460 controls were included in the study. Daily concentrations of CO, NO2, SO2, O3, PM2.5 and PM10 during the first trimester of pregnancy were assigned to each subject using the nearest monitoring station method. Multivariate logistic regression models were applied to evaluate the associations of monthly average exposure to gaseous air pollutants with orofacial clefts and its subtypes before and after adjusting for particulate matter. Variance inflation factors (VIFs) were used to determine if the effects of gaseous air pollutants could be independent of particulate matter. RESULTS: Increase in CO, NO2 and SO2 significantly increased the risk of cleft lip with or without cleft palate (CL/P) in all months during the first trimester of pregnancy, with aORs ranging from 1.39 to 1.48, from 1.35 to 1.61 and from 1.22 to 1.35, respectively. The risk of cleft palate only (CPO) increased with increasing NO2 exposure levels in the first trimester of pregnancy, with aORs ranging from 1.60 to 1.66. These effects sustained and even exacerbated after adjusting for particulate matter. No significant effect of O3 was observed. CONCLUSIONS: Our study suggested that maternal exposure to CO, NO2, and SO2 during the first trimester of pregnancy might contribute to the development of orofacial clefts, and the associations were potentially independent of particulate matter.

Overexpression of the essential Sis1 chaperone reduces TDP-43 effects on toxicity and proteolysis.

Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease characterized by selective loss of motor neurons with inclusions frequently containing the RNA/DNA binding protein TDP-43. Using a yeast model of ALS exhibiting TDP-43 dependent toxicity, we now show that TDP-43 overexpression dramatically alters cell shape and reduces ubiquitin dependent proteolysis of a reporter construct. Furthermore, we show that an excess of the Hsp40 chaperone, Sis1, reduced TDP-43's effect on toxicity, cell shape and proteolysis. The strength of these effects was influenced by the presence of the endogenous yeast prion, [PIN+]. Although overexpression of Sis1 altered the TDP-43 aggregation pattern, we did not detect physical association of Sis1 with TDP-43, suggesting the possibility of indirect effects on TDP-43 aggregation. Furthermore, overexpression of the mammalian Sis1 homologue, DNAJB1, relieves TDP-43 mediated toxicity in primary rodent cortical neurons, suggesting that Sis1 and its homologues may have neuroprotective effects in ALS.

Coping strategies and associated factors among older Chinese people living with HIV/AIDS.

Coping strategies play a prominent role in maintaining mental health, but little is known about the main coping strategies and potential influential factors among older Chinese adults with HIV/AIDS. Cross-sectional data of 254 older with HIV/AIDS aged 50 ~ 84 years (160 males and 94 females) from Hunan, China were analyzed to evaluate influential factors associated with coping strategies. The scores of all participants in the different sub-scales of confrontation, avoidance and acceptance-resignation were 15.16 ± 4.03, 16.44 ± 2.70, and 11.06 ± 4.00, respectively. For the confrontation coping strategy, higher scores were obtained by those with a higher education level, non-sexually transmitted HIV, and a first diagnosis at less than 50 years old. Avoidance as a coping strategy was significantly associated with a longer period living with the diagnosis. The participants who were females, unemployed, annual income less than 1000 yuan, had lived with HIV for a longer period, and had disclosed their infection status to their family members were more likely to adopt the acceptance-resignation coping strategy in response to HIV/AIDS. These preliminary findings can provide evidence for effective interventions to improve coping capacity and psychological status in this population.

QTL analysis and candidate gene identification for plant height in cotton based on an interspecific backcross inbred line population of Gossypium hirsutum × Gossypium barbadense.

KEY MESSAGE: We constructed the first high-quality and high-density genetic linkage map for an interspecific BIL population in cotton by specific-locus amplified fragment sequencing for QTL mapping. A novel gene GhPIN3 for plant height was identified in cotton. Ideal plant height (PH) is important for improving lint yield and mechanized harvesting in cotton. Most published genetic studies on cotton have focused on fibre yield and quality traits rather than PH. To facilitate the understanding of the genetic basis in PH, an interspecific backcross inbred line (BIL) population of 250 lines derived from upland cotton (Gossypium hirsutum L.) CRI36 and Egyptian cotton (G. barbadense L.) Hai7124 was used to construct a high-density genetic linkage map for quantitative trait locus (QTL) mapping. The high-density genetic map harboured 7,709 genotyping-by-sequencing (GBS)-based single nucleotide polymorphism (SNP) markers that covered 3,433.24 cM with a mean marker interval of 0.67 cM. In total, ten PH QTLs were identified and each explained 4.27-14.92% of the phenotypic variation, four of which were stable as they were mapped in at least two tests or based on best linear unbiased prediction in seven field tests. Based on functional annotation of orthologues in Arabidopsis and transcriptome data for the genes within the stable QTL regions, GhPIN3 encoding for the hormone auxin efflux carrier protein was identified as a candidate gene located in the stable QTL qPH-Dt1-1 region. A qRT-PCR analysis showed that the expression level of GhPIN3 in apical tissues was significantly higher in four short-statured cotton genotypes than that in four tall-statured cotton genotypes. Virus-induced gene silencing cotton has significantly increased PH when the expression of the GhPIN3 gene was suppressed.

Differentially expressed genes between two groups of backcross inbred lines differing in fiber length developed from Upland × Pima cotton.

Fiber length is one of the most important fiber quality traits in Upland cotton (Gossypium hirsutum L.), the most important fiber crop, and its improvement has been impeded in part by a lack of knowledge regarding its genetic basis. Introgressed backcross inbred lines (BILs) or near isogenic lines (NILs) differing in fiber length in the same genetic background, developed through advanced backcrossing between Upland cotton and extra-long staple cotton (G. barbadense L.), provide an important genomic resource for studying the molecular genetic basis of fiber length. In the present study, a long-fiber group and a short-fiber group, each with five BILs of Upland cotton, were selected from a BIL population between G. hirsutum and G. barbadense. Through a microarray-based comparative transcriptome analysis of developing fibers at 10 days postanthesis from the two groups, 1478 differentially expressed genes (DEGs) were identified. A total of 166 DEGs were then mapped to regions of fiber length quantitative trait loci (QTL), including 12 QTL hotspots and 2 QTL identified previously in the BIL population from which the two sets of BILs were selected. Several candidate genes possibly underlying the genetic control of fiber length differences between G. barbadense and G. hirsutum, including GhACX and GhKIF, were identified in this study. These results provide a list of positional candidate genes for the fine-scale mapping and map-based cloning of fiber length QTL, which will facilitate targeted gene transfer from G. barbadense to Upland cotton to further improve fiber quality.

Genetic variation of dynamic fiber elongation and developmental quantitative trait locus mapping of fiber length in upland cotton (Gossypium hirsutum L.).

BACKGROUND: In upland cotton (Gossypium hirsutum L.), genotypes with the same mature fiber length (FL) might possess different genes and exhibit differential expression of genes related to fiber elongation at different fiber developmental stages. However, there is a lack of information on the genetic variation influencing fiber length and its quantitative trait loci (QTLs) during the fiber elongation stage. In this study, a subset of upland cotton accessions was selected based on a previous GWAS conducted in China and grown in multiple environments to determine the dynamic fiber length at 10, 15, 20, and 25 days post-anthesis (DPA) and maturity. The germplasm lines were genotyped with the Cotton 63 K Illumina single-nucleotide polymorphism (SNP) array for GWAS. RESULTS: A total of 25, 38, 57, 89 and 88 SNPs showed significant correlations with fiber length at 10, 15, 20 and 25 DPA and maturity, respectively. In addition, 60 more promising SNPs were detected in at least two tests and two FL developmental time points, and 20 SNPs were located within the confidence intervals of QTLs identified in previous studies. The fastest fiber-length growth rates were obtained at 10 to 15 DPA in 69 upland cotton lines and at 15 to 20 DPA in 14 upland cotton accessions, and 10 SNPs showed significant correlations with the fiber-length growth rate. A combined transcriptome and qRT-PCR analysis revealed that two genes (D10G1008 and D13G2037) showed differential expression between two long-fiber genotypes and two short-fiber genotypes. CONCLUSIONS: This study provides important new insights into the genetic basis of the time-dependent fiber-length trait and reveals candidate SNPs and genes for improving fiber length in upland cotton.

Hetero-fertilization together with failed egg-sperm cell fusion supports single fertilization involved in in vivo haploid induction in maize.

In vivo doubled-haploid technology is widely applied in commercial maize breeding programs because of its time-saving and cost-reducing features. The production of maize haploids primarily depends on the use of Stock6-derived haploid inducer lines. Although the gene underlying haploid induction, MTL/ZmPLA1/NLD, was cloned recently, the mechanism of haploid induction is still unknown. Hetero-fertilization can occur via a single fertilization, which provides a means to investigate single-fertilization events by studying the hetero-fertilization phenomenon. In this study, we found that the hetero-fertilization rate increased significantly when female maize lines were first individually crossed with pollen from the inducer CAU5 in dual-pollination experiments 4 h before a second pollination with common lines. We also examined embryogenesis during haploid induction by confocal laser-scanning microscopy and observed single-fertilized ovules, indicating that single fertilization occurred during haploid induction. We therefore postulate that both single fertilization and chromosome elimination contribute to haploid induction in maize. We also propose a scheme for the formation of hetero-fertilized and haploid kernels. Our results provide an efficient approach to identify hetero-fertilized kernels for research on interactions between embryo and endosperm.

Amelioration of toxicity in neuronal models of amyotrophic lateral sclerosis by hUPF1.

Over 30% of patients with amyotrophic lateral sclerosis (ALS) exhibit cognitive deficits indicative of frontotemporal dementia (FTD), suggesting a common pathogenesis for both diseases. Consistent with this hypothesis, neuronal and glial inclusions rich in TDP43, an essential RNA-binding protein, are found in the majority of those with ALS and FTD, and mutations in TDP43 and a related RNA-binding protein, FUS, cause familial ALS and FTD. TDP43 and FUS affect the splicing of thousands of transcripts, in some cases triggering nonsense-mediated mRNA decay (NMD), a highly conserved RNA degradation pathway. Here, we take advantage of a faithful primary neuronal model of ALS and FTD to investigate and characterize the role of human up-frameshift protein 1 (hUPF1), an RNA helicase and master regulator of NMD, in these disorders. We show that hUPF1 significantly protects mammalian neurons from both TDP43- and FUS-related toxicity. Expression of hUPF2, another essential component of NMD, also improves survival, whereas inhibiting NMD prevents rescue by hUPF1, suggesting that hUPF1 acts through NMD to enhance survival. These studies emphasize the importance of RNA metabolism in ALS and FTD, and identify a uniquely effective therapeutic strategy for these disorders.

A genome-wide analysis of the lysophosphatidate acyltransferase (LPAAT) gene family in cotton: organization, expression, sequence variation, and association with seed oil content and fiber quality.

BACKGROUND: Lysophosphatidic acid acyltransferase (LPAAT) encoded by a multigene family is a rate-limiting enzyme in the Kennedy pathway in higher plants. Cotton is the most important natural fiber crop and one of the most important oilseed crops. However, little is known on genes coding for LPAATs involved in oil biosynthesis with regard to its genome organization, diversity, expression, natural genetic variation, and association with fiber development and oil content in cotton. RESULTS: In this study, a comprehensive genome-wide analysis in four Gossypium species with genome sequences, i.e., tetraploid G. hirsutum- AD1 and G. barbadense- AD2 and its possible ancestral diploids G. raimondii- D5 and G. arboreum- A2, identified 13, 10, 8, and 9 LPAAT genes, respectively, that were divided into four subfamilies. RNA-seq analyses of the LPAAT genes in the widely grown G. hirsutum suggest their differential expression at the transcriptional level in developing cottonseeds and fibers. Although 10 LPAAT genes were co-localised with quantitative trait loci (QTL) for cottonseed oil or protein content within a 25-cM region, only one single strand conformation polymorphic (SSCP) marker developed from a synonymous single nucleotide polymorphism (SNP) of the At-Gh13LPAAT5 gene was significantly correlated with cottonseed oil and protein contents in one of the three field tests. Moreover, transformed yeasts using the At-Gh13LPAAT5 gene with the two sequences for the SNP led to similar results, i.e., a 25-31% increase in palmitic acid and oleic acid, and a 16-29% increase in total triacylglycerol (TAG). CONCLUSIONS: The results in this study demonstrated that the natural variation in the LPAAT genes to improving cottonseed oil content and fiber quality is limited; therefore, traditional cross breeding should not expect much progress in improving cottonseed oil content or fiber quality through a marker-assisted selection for the LPAAT genes. However, enhancing the expression of one of the LPAAT genes such as At-Gh13LPAAT5 can significantly increase the production of total TAG and other fatty acids, providing an incentive for further studies into the use of LPAAT genes to increase cottonseed oil content through biotechnology.

A genome-wide analysis of the small auxin-up RNA (SAUR) gene family in cotton.

BACKGROUND: Small auxin-up RNA (SAUR) gene family is the largest family of early auxin response genes in higher plants, which have been implicated in the regulation of multiple biological processes. However, no comprehensive analysis of SAUR genes has been reported in cotton (Gossypium spp.). RESULTS: In the study, we identified 145, 97, 214, and 176 SAUR homologous genes in the sequenced genomes of G. raimondii, G. arboreum, G. hirsutum, and G. barbadense, respectively. A phylogenetic analysis revealed that the SAUR genes can be classified into 10 groups. A further analysis of chromosomal locations and gene duplications showed that tandem duplication and segmental duplication events contributed to the expansion of the SAUR gene family in cotton. An exon-intron organization and motif analysis revealed the conservation of SAUR-specific domains, and the auxin responsive elements existed in most of the upstream sequences. The expression levels of 16 GhSAUR genes in response to an exogenous application of IAA were determined by a quantitative RT-PCR analysis. The genome-wide RNA-seq data and qRT-PCR analysis of selected SAUR genes in developing fibers revealed their differential expressions. The physical mapping showed that 20 SAUR genes were co-localized with fiber length quantitative trait locus (QTL) hotspots. Single nucleotide polymorphisms (SNPs) were detected for 12 of these 20 genes between G. hirsutum and G. barbadense, but no SNPs were identified between two backcross inbred lines with differing fiber lengths derived from a cross between the two cultivated tetraploids. CONCLUSIONS: This study provides an important piece of genomic information for the SAUR genes in cotton and lays a solid foundation for elucidating the functions of SAUR genes in auxin signaling pathways to regulate cotton growth.