Genome-wide identification and characterization of FAD family genes in barley.

Fatty acid desaturases (FADs) play pivotal roles in determining plant stress tolerance. Barley is the most salt-tolerant cereal crop. In this study, we performed genome-wide identification and characterization analysis of the FAD gene family in barley (Hordeum vulgare). A total of 24 HvFADs were identified and divided into four subfamilies based on their amino acid sequence similarity. HvFADs unevenly distributed on six of seven barley chromosomes, and three clusters of HvFADs mainly occurred on the chromosome 2, 3 and 6. Segmental duplication events were found to be a main cause for the HvFAD gene family expansion. The same HvFAD subfamily showed the relatively consistent exon-intron composition and conserved motifs of HvFADs. Cis-element analysis in HvFAD promoters indicated that the expression of HvFADs may be subject to complex regulation, especially stress-responsive elements that may involve in saline-alkaline stress response. Combined transcriptomic data with quantitative experiments, at least five HvFADs highly expressed in roots under salt or alkali treatment, suggesting they may participate in saline or alkaline tolerance in barley. This study provides novel and valuable insights for underlying salt/alkali-tolerant mechanisms in barley.

A designer synthetic chromosome fragment functions in moss.

Rapid advances in DNA synthesis techniques have enabled the assembly and engineering of viral and microbial genomes, presenting new opportunities for synthetic genomics in multicellular eukaryotic organisms. These organisms, characterized by larger genomes, abundant transposons and extensive epigenetic regulation, pose unique challenges. Here we report the in vivo assembly of chromosomal fragments in the moss Physcomitrium patens, producing phenotypically virtually wild-type lines in which one-third of the coding region of a chromosomal arm is replaced by redesigned, chemically synthesized fragments. By eliminating 55.8% of a 155 kb endogenous chromosomal region, we substantially simplified the genome without discernible phenotypic effects, implying that many transposable elements may minimally impact growth. We also introduced other sequence modifications, such as PCRTag incorporation, gene locus swapping and stop codon substitution. Despite these substantial changes, the complex epigenetic landscape was normally established, albeit with some three-dimensional conformation alterations. The synthesis of a partial multicellular eukaryotic chromosome arm lays the foundation for the synthetic moss genome project (SynMoss) and paves the way for genome synthesis in multicellular organisms.

The complete chloroplast genome of Hordeum marinum ssp. marinum.

Hordeum marinum ssp. marinum (Huds.) R. J. Soreng (2003) is a halophyte wild relative of barley and wheat, which exhibits remarkable salt tolerance characteristics. In this study, we presented the first characterization of the complete chloroplast genome of H. marinum ssp. marinum. Our findings reveal that the chloroplast genome of H. marinum ssp. marinum consists of a small single-copy region (SSC: 12,715 bp), a large single-copy region (LSC: 81,130 bp), and a pair of inverted repeat regions (IRs: 21,517 bp), amounting to a total length of 136,989 bp. The chloroplast genome encodes 139 genes, including 91 protein-coding genes, 38 tRNA genes, and ten rRNA genes. By utilizing phylogenetic analysis, we determine the evolutionary position of H. marinum in Triticeae. Our study provides valuable insights into the chloroplast genome of H. marinum ssp. marinum, which may have important implications for the improvement of cereal crops.

Condensation of STM is critical for shoot meristem maintenance and salt tolerance in Arabidopsis.

The shoot meristem generates the entire shoot system and is precisely maintained throughout the life cycle under various environmental challenges. In this study, we identified a prion-like domain (PrD) in the key shoot meristem regulator SHOOT MERISTEMLESS (STM), which distinguishes STM from other related KNOX1 proteins. We demonstrated that PrD stimulates STM to form nuclear condensates, which are required for maintaining the shoot meristem. STM nuclear condensate formation is stabilized by selected PrD-containing STM-interacting BELL proteins in vitro and in vivo. Moreover, condensation of STM promotes its interaction with the Mediator complex subunit MED8 and thereby enhances its transcriptional activity. Thus, condensate formation emerges as a novel regulatory mechanism of shoot meristem functions. Furthermore, we found that the formation of STM condensates is enhanced upon salt stress, which allows enhanced salt tolerance and increased shoot branching. Our findings highlight that the transcription factor partitioning plays an important role in cell fate determination and might also act as a tunable environmental acclimation mechanism.

Stochastic gene expression drives mesophyll protoplast regeneration.

Cell pluripotency is fundamental to biology. It has long been known that differentiated somatic plant cells may reacquire pluripotency, but the underlying mechanism remains elusive. In many plant species, a single isolated mesophyll protoplast may regenerate into an entire plant, which is widely used in gene transformation. Here, we identified two transcription factors whose ectopic activation promotes protoplast regeneration. Furthermore, we found that their expression was induced by protoplast isolation but at a very low frequency. Using live imaging and single-cell transcriptomics, we show that isolating protoplasts induces enhanced expression variation at the genome level. Isolating protoplasts also leads to genome-wide increases in chromatin accessibility, which promotes stochastic activation of gene expression and enhances protoplast regeneration. We propose that transcriptome chaos with increased expression variability among cells creates a cellular-level evolutionary driver selecting for regenerating cells.

TheraSling Therapy (TST) Combined with Neuromuscular Facilitation Technique on Hemiplegic Gait in Patients with Stroke.

BACKGROUND TheraSling therapy (TST) is a kind of rehabilitation therapy for patients with stroke in order to improving neural function. The aim of this study was to evaluate the clinical efficacy of TST combined with neuromuscular facilitation technique on hemiplegic gait in patients with stroke. MATERIAL AND METHODS Fifty-six patients with abnormal gait after stroke were recruited for this study and assigned randomly to either the control group (n=28) or the TST experiment group (n=28). Patients in the 2 groups all received neuromuscular facilitation technique treatment. In addition, patients in the TST experiment group were received TST. Treatments were 45 minutes a day for 6 weeks. RESULTS The functional ambulation category (FAC) score, improved Barthel index, Fugl-Meyer assessment (FMA), Berg balance scale (BBS), and 10 meters walking time and step length were significantly improve in both the TST experiment group and the control group after 6 weeks of treatment with a statistical difference (P<0.05). And the aforementioned indices in the TST experiment group after treatment were significantly higher than those of control group (P<0.05). CONCLUSIONS Lower extremity motor function and quality of life were significantly improved by TST combined with neuromuscular facilitation technique. However, the study had a small sample size, thus, further multicenter well-designed prospective randomized controlled trials are needed to confirm our findings.

A gene expression map of shoot domains reveals regulatory mechanisms.

Gene regulatory networks control development via domain-specific gene expression. In seed plants, self-renewing stem cells located in the shoot apical meristem (SAM) produce leaves from the SAM peripheral zone. After initiation, leaves develop polarity patterns to form a planar shape. Here we compare translating RNAs among SAM and leaf domains. Using translating ribosome affinity purification and RNA sequencing to quantify gene expression in target domains, we generate a domain-specific translatome map covering representative vegetative stage SAM and leaf domains. We discuss the predicted cellular functions of these domains and provide evidence that dome seemingly unrelated domains, utilize common regulatory modules. Experimental follow up shows that the RABBIT EARS and HANABA TARANU transcription factors have roles in axillary meristem initiation. This dataset provides a community resource for further study of shoot development and response to internal and environmental signals.

Chiral Phosphine-Phosphite Ligands in Asymmetric Gold Catalysis: Highly Enantioselective Synthesis of Furo[3,4-d]-Tetrahydropyridazine Derivatives through [3+3]-Cycloaddition.

The AuI -catalyzed reaction of 2-(1-alkynyl)-2-alken-1-ones with azomethine imines regio- and diastereoselectively affords furo[3,4-d]tetrahydropyridazines in a tandem cyclization/intermolecular [3+3]-cycloaddition process under mild conditions. By employing a chiral gold catalyst (prepared in situ from a Taddol-derived phosphine-phosphite ligand, Me2 SAuCl, and AgOTf) high yields and enantioselectivities (up to 94 % yield, up to 96 % ee) are obtained. The method provides an efficient modular route to substituted heterotricyclic furan derivatives and can be easily scaled up (using catalyst loads of only 0.15 mol %).

Long noncoding RNA hypoxia-inducible factor 1 alpha-antisense RNA 1 promotes tumor necrosis factor-α-induced apoptosis through caspase 3 in Kupffer cells.

Kupffer cells (KCs) play a crucial role in the pathogenesis of acute-on-chronic liver failure (ACLF) which is characterized by acute and severe disease in patients with preexisting liver disease and shows high mortality. Long noncoding RNAs (lncRNAs) are recently found to be involved in gene regulation. However, the mechanisms of how KCs are regulated by inflammatory factors, tumor necrosis factor-α (TNF-α), and whether lncRNAs are involved in the process remain largely unknown. Hence, we investigated the role of lncRNAs in the cytotoxicity of TNF-α on KCs.lncRNA array (The lncRNAs in the array are apoptosis-related lncRNAs reported in some research papers.) was used to identify lncRNAs related with liver fibrosis. Annexin V/protease inhibitor (PI) staining was used for detection of cell apoptosis. Real time-polymerase chain reaction was utilized for analysis of mRNA levels of lncRNA hypoxia-inducible factor 1 alpha-antisense RNA 1 (HIF1A-AS1) and apoptosis-related genes. Western blot was implied to the determination of lymphoid enhancer factor-1 (LEF-1).In this study, we found that HIF1A-AS1 could be upregulated by TNF-α by lncRNA array analysis and knockdown of HIF1A-AS1 significantly rescued cell apoptosis induced by TNF-α. Moreover, inhibition of HIF1A-AS1 markedly reduced mRNA level of caspase 3 which can be significantly enhanced by TNF-α. Furthermore, HIF1A-AS1 showed binding sites for LEF-1 and siRNA-mediated downregulation of LEF-1 decreased HIF1A-AS1 level in KCs treated with TNF-α.This study elucidates a new role of HIF1A-AS1 in TNF-α-induced cell apoptosis and provides potential therapeutic targets for ACLF.

Complete mitochondrial genome of Rhynchophorus ferrugineus.

In this study, we determined the mitochondrial genome of Rhynchophorus ferrugineus. The mitochondrial genome is 15 924 bp in length (GC content: 25.6%), encodes 2 ribosomal RNA genes, 13 protein-coding genes, 21 transfer RNA genes, and 1 D-loop region. nad6 and cob are overlapped by 30 bp and atp8 and atp6 are overlapped by 12 bp. The phylogenetic tree involving 29 available closely related species further validated the new determined sequences and phylogeny of R. ferrugineus.

The complete mitochondrial genome of Batrachoseps nigriventris (Caudata: Plethodontidae).

Batrachoseps nigriventris was classified in order Caudata, family Plethodontidae. In this study, we obtained the complete mitochondrial genome sequence of B. nigriventris, which was 17 403 bp in length. With a base composition of 33.5%A, 30.9%T, 21.4%C, and 14.2%G, this genome contained 13 protein-coding genes (PCGs), 23 transfer RNA genes (tRNA), 2 ribosomal RNA genes (rRNA), and 1 control region (D-loop) . Phylogenetic analysis was performed using protein-coding genes cox1, combined with other 28 closely related species to assess their phylogenic relationship. This mitochondrial genome sequence will provide a better understanding for B. nigriventris evolution in the future.

Complete mitochondrial genome of the argentine ant, Linepithema humile (Hymenoptera: Formicidae).

In this study, the complete mitochondrial genome of the widespread invasive Argentine ant (Linepithema humile) was first determined. The mitochondrial genome is 16 098 bp in length, and encodes one D-loop region, two ribosomal RNA genes, 13 protein-coding genes, and 18 transfer RNA genes. Average GC content of this genome is 19.68%. nad6 and cob genes were overlapped by 4 bp. The phylogenetic tree involving 13 available closely related species further validated the new determined sequences and phylogeny of L. humile.

Association of Rs2071410 on Furin with Transient Ischemic Attack Susceptibility and Prognosis in a Chinese Population.

BACKGROUND Because genotype CG/GG of Furin rs2071410 can increase susceptibility to hypertension, this study investigated whether Furin rs2071410 is correlated with transient ischemic attack (TIA) susceptibility and prognosis. MATERIAL AND METHODS The odds ratios (ORs) and their 95% confidence intervals (95% CIs) were evaluated to assess the association of rs2071410 with TIA risk, and logistic regression was used to estimate the effects of various risk factors (e.g., diabetes, hypertension, and hyperlipidemia) on TIA. RESULTS Compared with the homozygous genotype CC of rs2071410, the frequency of CG + GG genotype in the case group was significantly higher than in the control group (OR=1.47, 95% CI: 1.05-2.05, P<0.05). The CG + GG genotype carriers were observed to have worse 90-day prognosis after TIA treatment than patients carrying CC genotype (OR=12.86, 95% CI: 7.41-22.33, P<0.05). Moreover, logistic regression analysis found that age, diabetes, hypertension, and hyperlipidemia were associated with the onset of TIA (P<0.05, all). Of note, individuals with CG + GG genotype had 49.3% increased risk of TIA compared with individuals with CC genotype (OR=1.49, 95% CI: 1.05-2.12), and patients with CG + GG genotype had worse 90-day prognosis after TIA treatment than patients with CC genotype (OR=11.39, 95% CI: 6.29-20.62). CONCLUSIONS Furin rs2071410 was significantly correlated with TIA occurrence and prognosis in the Chinese population.

The complete chloroplast genome of Gracilariopsis lemaneiformis (Rhodophyta) gives new insight into the evolution of family Gracilariaceae.

The complete chloroplast genome of Gracilariopsis lemaneiformis was recovered from a Next Generation Sequencing data set. Without quadripartite structure, this chloroplast genome (183,013 bp, 27.40% GC content) contains 202 protein-coding genes, 34 tRNA genes, 3 rRNA genes, and 1 tmRNA gene. Synteny analysis showed plasmid incorporation regions in chloroplast genomes of three species of family Gracilariaceae and in Grateloupia taiwanensis of family Halymeniaceae. Combined with reported red algal plasmid sequences in nuclear and mitochondrial genomes, we postulated that red algal plasmids may have played an important role in ancient horizontal gene transfer among nuclear, chloroplast, and mitochondrial genomes. Substitution rate analysis showed that purifying selective forces maintaining stability of protein-coding genes of nine red algal chloroplast genomes over long periods must be strong and that the forces acting on gene groups and single genes of nine red algal chloroplast genomes were similar and consistent. The divergence of Gp. lemaneiformis occurred ~447.98 million years ago (Mya), close to the divergence time of genus Pyropia and Porphyra (443.62 Mya).

Effects of sodium bicarbonate concentration on growth, photosynthesis, and carbonic anhydrase activity of macroalgae Gracilariopsis lemaneiformis, Gracilaria vermiculophylla, and Gracilaria chouae (Gracilariales, Rhodophyta).

There is potential for bicarbonate to improve crop yields and economic efficiency of marine algae. However, few studies have focused on the effect of bicarbonate on the growth, photosynthesis, and enzyme activity associated with carbon utilization, especially in commercial macroalgae. Here, the addition of bicarbonate (up to 420 mg L(-1)) to macroalgal cultures has been evaluated for Gracilariopsis lemaneiformis, Gracilaria vermiculophylla, and Gracilaria chouae with respect to growth rate, photosynthetic activity, carbonic anhydrase activity, and biochemical composition. The results showed that the effects of NaHCO3 on growth, chlorophyll a, phycoerythrin, photosynthetic oxygen evolution, photochemical parameters of PSI and PSII, carbonic anhydrase activity, and nitrogen content were significant (P < 0.05) and followed the same pattern in the three species. The parameter values were promoted in lower NaHCO3 concentrations (up to 252 or 336 mg L(-1)) and inhibited in higher NaHCO3 concentrations (>336 mg L(-1) for Gp. lemaneiformis and >420 mg L(-1) for the other two species). Moreover, species-specific differences induced by supplementation with bicarbonate were discovered during culture. Optimal concentrations of NaHCO3 used in this study were 252 mg L(-1) for Gp. lemaneiformis and 336 mg L(-1) for G. vermiculophylla and G. chouae. These results suggest that an adequate supplementation of sodium bicarbonate is a viable strategy for promoting growth and photosynthetic activity in some macroalgae as well as for improving biochemical composition. The study will help to accelerate the growth rate of algae and improve the quality of thalli, and will also be useful for enhancing the understanding of carbon utilization in macroalgae.

New role and molecular mechanism of Gadd45a in hepatic fibrosis.

AIM: To investigate the role of Gadd45a in hepatic fibrosis and the transforming growth factor (TGF)-ß/Smad signaling pathway. METHODS: Wild-type male BALB/c mice were treated with CCl4 to induce a model of chronic liver injury. Hepatic stellate cells (HSCs) were isolated from the liver of BALB/c mice and were treated with small interfering RNAs (siRNAs) targeting Gadd45a or the pcDNA3.1-Gadd45a recombinant plasmid. Cellular α-smooth muscle actin (α-SMA), ß-actin, type I collagen, phospho-Smad2, phospho-Smad3, Smad2, Smad3, and Smad4 were detected by Western blots. The mRNA levels of α-SMA, ß-actin, and type I collagen were determined by quantitative real-time (qRT)-PCR analyses. Reactive oxygen species production was monitored by flow cytometry using 2,7-dichlorodihydrofluorescein diacetate. Gadd45a, Gadd45b, anti-Gadd45g, type I collagen, and SMA local expression in liver tissue were measured by histologic and immunohistochemical analyses. RESULTS: Significant downregulation of Gadd45a, but not Gadd45b or Gadd45g, accompanied by activation of the TGF-ß/Smad signaling pathways was detected in fibrotic liver tissues of mice and isolated HSCs with chronic liver injury induced by CCl4 treatment. Overexpression of Gadd45a reduced the expression of extracellular matrix proteins and α-SMA in HSCs, whereas transient knockdown of Gadd45a with siRNA reversed this process. Gadd45a inhibited the activity of a plasminogen activator inhibitor-1 promoter construct and (CAGA)9 MLP-Luc, an artificial Smad3/4-specific reporter, as well as reduced the phosphorylation and nuclear translocation of Smad3. Gadd45a showed protective effects by scavenging reactive oxygen species and upregulating antioxidant enzymes. CONCLUSION: Gadd45a may counteract hepatic fibrosis by regulating the activation of HSCs via the inhibition of TGF-ß/Smad signaling.

Complete mitochondrial genome of Bombus terrestris (Hymenoptera: Apidae).

In this study, complete mitochondrial genome of the large earth bumblebee, Bombus terrestris, was first determined. The mitochondrial genome is 174 000 bp in length, and encodes 1 D-loop region, 2 ribosomal RNA genes, 13 protein-coding genes and 20 transfer RNA genes. Average GC content of this genome is 15%. nad6 and cob are overlapped with 12 bp, while atp8 and atp6 are overlapped with 18 bp. Phylogeny analysis indicates Bombus species exhibit closer genetic distance with Melipona species than with Apis species.

Momordin Ic couples apoptosis with autophagy in human hepatoblastoma cancer cells by reactive oxygen species (ROS)-mediated PI3K/Akt and MAPK signaling pathways.

Momordin Ic is a principal saponin constituent of Fructus Kochiae, which acts as an edible and pharmaceutical product more than 2000 years in China. Our previous research found momordin Ic induced apoptosis by PI3K/Akt and MAPK signaling pathways in HepG2 cells. While the role of autophagy in momordin Ic induced cell death has not been discussed, and the connection between the apoptosis and autophagy is not clear yet. In this work, we reported momordin Ic promoted the formation of autophagic vacuole and expression of Beclin 1 and LC-3 in a dose- and time-dependent manner. Compared with momordin Ic treatment alone, the autophagy inhibitor 3-methyladenine (3-MA) also can inhibit apoptosis, while autophagy activator rapamycin (RAP) has the opposite effect, and the apoptosis inhibitor ZVAD-fmk also inhibited autophagy induced by momordin Ic. Momordin Ic simultaneously induces autophagy and apoptosis by suppressing the ROS-mediated PI3K/Akt and activating the ROS-related JNK and P38 pathways. Additionally, momordin Ic induces apoptosis by suppressing PI3K/Akt-dependent NF-κB pathways and promotes autophagy by ROS-mediated Erk signaling pathway. Those results suggest that momordin Ic has great potential as a nutritional preventive strategy in cancer therapy.

Complete mitochondrial genome of a red calcified alga Calliarthron tuberculosum (Corallinales).

454 GS FLX Titanium sequencing data were used to obtain the complete mitochondrial genome of Calliarthron tuberculosum (26,469 bp). The mitogenome contains 44 genes, including 2 ribosomal RNA, 19 transfer RNA, 5 ribosomal proteins, 1 ymf, 2 open reading frames (ORFs) and 16 genes involved in cellular respiration. The secY and rps12 are overlapped by 69 bp. rps3 and rpl16 also have a 45 bp overlapped region. Except for open reading frames near stem-loop region, the results show Calliarthron tuberculosum mtDNA has a high similarity with other Florideophyceae algae mitogenomes in gene synteny, structure and gene content. Phylogeny analysis indicates a close genetic relationship of Calliarthron tuberculosum with Sporolithon durum.

Complete mitochondrial genome of Plodia interpunctella (Lepidoptera: Pyralidae).

The complete mitochondrial genome sequence of Plodia Interpunctella (Lepidoptera: Pyralidae) was determined. The circular genome has a size of 15 733 base pairs, containing 36 gene protein-coding genes, two rRNA genes, and 21 tRNA genes. The overall base composition was 41.37% of A, 37.99% of T, 12.54% of G, and 8.10% of C. Furthermore, a phylogenetic tree was constructed based on complete mitogenomes of Plodia interpunctella and 11 closely related Pyralidae species to validate the taxonomy relationship. The complete mitochondrial genome of the P. interpunctella would provide more information for the evolution of Pyralidae family.