Ancient Mitogenomes Reveal the Maternal Genetic History of East Asian Dogs.

Recent studies have suggested that dogs were domesticated during the Last Glacial Maximum (LGM) in Siberia, which contrasts with previous proposed domestication centers (e.g. Europe, the Middle East, and East Asia). Ancient DNA provides a powerful resource for the study of mammalian evolution and has been widely used to understand the genetic history of domestic animals. To understand the maternal genetic history of East Asian dogs, we have made a complete mitogenome dataset of 120 East Asian canids from 38 archaeological sites, including 102 newly sequenced from 12.9 to 1 ka BP (1,000 years before present). The majority (112/119, 94.12%) belonged to haplogroup A, and half of these (55/112, 49.11%) belonged to sub-haplogroup A1b. Most existing mitochondrial haplogroups were present in ancient East Asian dogs. However, mitochondrial lineages in ancient northern dogs (northeastern Eurasia and northern East Asia) were deeper and older than those in southern East Asian dogs. Results suggests that East Asian dogs originated from northeastern Eurasian populations after the LGM, dispersing in two possible directions after domestication. Western Eurasian (Europe and the Middle East) dog maternal ancestries genetically influenced East Asian dogs from approximately 4 ka BP, dramatically increasing after 3 ka BP, and afterwards largely replaced most primary maternal lineages in northern East Asia. Additionally, at least three major mitogenome sub-haplogroups of haplogroup A (A1a, A1b, and A3) reveal at least two major dispersal waves onto the Qinghai-Tibet Plateau in ancient times, indicating eastern (A1b and A3) and western (A1a) Eurasian origins.

Reproductive strategy response of the fungi Sarocladium and the evaluation for remediation under stress of heavy metal Cd(II).

Cadmium (Cd) is documented as one of the most lethal metals and poses a major threat to all life forms in the environment due to its toxic effects. Bioremediation of hazardous metals has received considerable and growing interest over the years. The functional fungi with tolerance to the heavy metal Cd were screened from the mining soil samples. Two fungi isolates from coal mine soil were characterized as Sarocladium sp. M2 and Sarocladium sp. M6 based on morphological and partial ITS sequencing analysis. M2 and M6 exhibited high levels of resistance to cadmium, and they were investigated for their micro-morphology and application in heavy metal removal with different concentration Cd(II) (0, 50, 100, 150 and 200 mg/L). The colony morphology of M2 and M6 gradually become very similar to that of bacteria with the increase of cadmium concentration (150-200 mg/L). Micro-morphological studies showed that Cd(II) exposure caused the disappearance of conidial heads and the occurrence of hyphae breakage (100-200 mg/L Cd(II), which is consistent to the colony morphology results. The surface/volume ratio of the spores decreased with the presence of Cd(II). The removal potential of fungi for cadmium was quantified by atomic absorption spectrometry. M2 and M6 showed great potential as bioremediators for highly Cd(II)-contaminated environment. The highest Cd(II) biosorption capacity was 5.13 ± 0.21 mg/g for M2 and 6.04 ± 0.21 mg/g for M6. The highest heavy metal sorption by M2 removed 57.11% ± 4.45% Cd(II) while that of M6 removed 48.35% ± 1.44% Cd(II) in 200 mg/L initial concentration Cd(II). To the best of our knowledge, this is the first report that cadmium induced the change of reproduction mode of the Sarocladium, from conidia to arthrospores, which made the colony morphological modifications, from the fungi colony morphology to the bacteria colony morphology. The arthrospore-modified (hyphae breakage) seemed to accumulate greater amounts of heavy metals than filamentous hyphae formation.

The haplotype-resolved autotetraploid genome assembly provides insights into the genomic evolution and fruit divergence in wax apple (Syzygium samarangense (Blume) Merr. and Perry).

Wax apple (Syzygium samarangense) is an economically important fruit crop with great potential value to human health because of its richness in antioxidant substances. Here, we present a haplotype-resolved autotetraploid genome assembly of the wax apple with a size of 1.59 Gb. Comparative genomic analysis revealed three rounds of whole-genome duplication (WGD) events, including two independent WGDs after WGT-γ. Resequencing analysis of 35 accessions partitioned these individuals into two distinct groups, including 28 landraces and seven cultivated species, and several genes subject to selective sweeps possibly contributed to fruit growth, including the KRP1-like, IAA17-like, GME-like, and FLACCA-like genes. Transcriptome analysis of three different varieties during flower and fruit development identified key genes related to fruit size, sugar content, and male sterility. We found that AP2 also affected fruit size by regulating sepal development in wax apples. The expression of sugar transport-related genes (SWEETs and SUTs) was high in 'ZY', likely contributing to its high sugar content. Male sterility in 'Tub' was associated with tapetal abnormalities due to the decreased expression of DYT1, TDF1, and AMS, which affected early tapetum development. The chromosome-scale genome and large-scale transcriptome data presented in this study offer new valuable resources for biological research on S. samarangense and shed new light on fruit size control, sugar metabolism, and male sterility regulatory metabolism in wax apple.

Mutations in Growth-Related Genes Induced by EMS Treatment in Scallops.

Background: The goal of genetic breeding is to select variants with mutations that are related to expected traits, such as fast growth. Artificial induction has been widely used to obtain strains with more mutations for further selection. Ethylmethylsulfone (EMS) is one of the most commonly used chemical mutagens in plant and microorganism breeding. However, the application of EMS mutagenesis in shellfish has not been reported. The aim of this study is to evaluate the potential use of EMS as a mutagen in scallop breeding, especially in characterization of mutations in growth-related genes. Results: Our results indicated that hatching of about 50% of fertilized eggs was blocked by treatment with 20 mM EMS for 3 h and the resulted larvae developed normally into adult stages. We then evaluated the mutagenic effects of EMS by sequencing the genomes of 4 adult scallops from the control group and 12 from the treatment group at 8 months after fertilization. On average, after removing shared types of mutations, there were 1,151,380 ± 258,188 SNPs (Single Nucleotide Polymorphisms) and 229,256 ± 51,714 InDels (insertion-deletion) in each animal in the EMS treatment group, while there were only134841 ± 10,115 SNPs and 42,605 ± 5,136 InDels in the control group. The average mutation rate in the genome of the EMS treatment group (0.0137 ± 0.0013%) was about 9 times that of the control group (0.0015 ± 0.0002%). GO (Gene Ontology) annotation and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analyses revealed that mutations induced by EMS occurred evenly in most biological processes, cellular components and functions, as well in most pathways. However, significant lower percentage of mutations were found in the exonic region, in non-synonymous or Stopgain/Stoploss SNPs and in coding domains, suggesting apparent DNA repair or selection during grow-out stage. Analyses of the growth-related genes with mutations indicated that mutations in MFS (Major Facilitator Superfamily) and Tubulin were only found in the large-sized group (Five largest scallops: Treated-1, Treated-2, Treated-3, Treated-4, and Treated-5) and Homeobox and Socs (Suppressor of cytokine signaling) only in the small group (Two smallest scallops: Treated-11 and Treated-12). These results suggested that these genes may be involved in the regulation of growth in these animals, although further verification is certainly warranted. Conclusion: Treatment of fertilized eggs with 20 mM EMS for 3 h induced 9 times more mutations in scallop genomes. We found that mutations in MFS and Tubulin may be related to fast growth in the large-sized group and those mutations in Homeobox and SOCs may be involved in the slow growth in the small-sized scallops. EMS can be used to accelerate selection of economically important traits in molluscs.

Characterization of the molecular mechanism underlying the dwarfism of dsh mutant watermelon plants.

Developing dwarf watermelon is a major objective among breeders. The dsh dwarf watermelon germplasm developed in our laboratory is genetically stable. We previously produced preliminary evidence that Cla010726, which encodes a gibberellin 20-oxidase-like protein, is the primary gene controlling dwarfism in watermelon. However, the underlying genetic mechanism was unknown. In this study, we characterized the spontaneous recessive mutant dsh, which is a gibberellin (GA)-deficient mutant. Many of the phenotypic traits of dsh plants are similar to those of known GA-deficient mutants. The dsh plants were sensitive to exogenous bioactive GAs, which increased seedling height. Moreover, a quantitative analysis of endogenous GA3 proved that the bioactive GA3 content was substantially lower than normal in dsh. Additionally, the T5ClaGA20ox RNAi plants generally exhibited dwarfism, with short stems and internodes as well as small leaves and fruit. An examination of the transgenic plants carrying the ClaGA20ox1 promoter-GUS and mutant ClaGA20ox2 promoter-GUS constructs confirmed that two promoter sites are involved in the regulation of ClaGA20ox expression. Hence, mutations in the promoter of the GA20ox gene, which encodes a key enzyme involved in gibberellin biosynthesis, lead to the dwarfism of watermelon plants. The dsh mutant is a potentially useful germplasm resource for developing new watermelon varieties exhibiting dwarfism.

Model for Predicting the Tortuosity of Transport Paths in Cement-Based Materials.

The tortuosity of the pore structure is an important factor affecting medium (water and harmful ions) transport in cement-based materials. In this study, a new tortuosity model was established to reveal the effect of aggregate size, morphology, and graded media on the transport path in cement-based materials. Based on the stereological principle and the geometric algorithm, the distribution model of the ideal pebble and polygonal aggregate in cement-based materials was given first. Then, based on the image processing technology and MATLAB software, the morphology of the actual aggregate was also characterized to prove the similarity relationship between the ideal aggregate and actual aggregate. The reliability of the tortuosity model was verified by the mercury intrusion porosimetry test and data from other literature. Based on the tortuosity model, the influences of the aggregate particle shape parameters, hydration degree, and water-to-cement ratio on the tortuosity of the transport path were analyzed. Finally, the tortuosity model was further simplified to facilitate engineering application.

Phosphine-Catalyzed Diastereo- and Enantioselective Michael Addition of ß-Carbonyl Esters to ß-Trifluoromethyl and ß-Ester Enones: Enhanced Reactivity by Inorganic Base.

A novel chiral biamide-phosphine multifunctional catalyst has been developed that mediates the asymmetric intermolecular Michael addition of ß-carbonyl esters to ß-trifluoromethyl enones and 3-aroyl acrylates in the presence of competing methyl acrylate and the inorganic base. This method provides a facile access to structurally diverse trifluoromethyl and quaternary stereogenic centers with excellent enantioselectivity (up to 99% ee) and good diastereoselectivity (up to 13:1 dr). The addition of the inorganic base (K3PO4) does not cause the background racemic reaction and enhances the reactivity by serving as a co-catalyst.

A novel selective inhibitor to thrombin-induced platelet aggregation purified from the leech Whitmania pigra.

BACKGROUND/AIM: The dried whole body of the leech Whitmania pigra, a well-known traditional Chinese medicine, has been widely used to treat thrombus diseases for thousands of years. However, its bioactive constituents were reported rarely. The aim of our study was to investigate antithrombotic components of it. METHODS: The antithrombotic peptide was purified using a combination of anion-exchange chromatography, ultrafiltration and reverse-phase HPLC. the sequence of the peptide was determined using MALDI-TOF-MS-MS. Anti-platelet aggregation activity in vitro was evaluated using a turbidimetric method, and antithrombotic effect in vivo was assessed in an arterio-venous shunt thrombosis model in rats. RESULTS: A novel antithrombotic peptide named WP-30, with the sequence VISRTQSNVQAAWGQVGGHAADYSAVAIER, was isolated from the dried whole body of the leech W. pigra. WP-30 selectively inhibited thrombin-induced anti-platelet aggregation in vitro, and potently attenuated thrombus formation in rats in vivo. CONCLUSIONS: Taken together, we found a novel peptide from leech bodies, and this peptide showed antiplatelet aggregation and antithrombotic effects.

Human cathelicidin LL-37 inhibits platelet aggregation and thrombosis via Src/PI3K/Akt signaling.

Biological functions of human cathelicidin LL-37 have been widely reported, including antibacterial, immune and anti-tumor effects. However, the antiplatelet activity of LL-37 has not been addressed. The purpose of our study was to investigate the antiplatelet and antithrombotic actions of LL-37. We found that this peptide inhibited human platelet aggregation in vitro and attenuated thrombus formation in vivo. Furthermore, LL-37 reduced phosphorylation of Src kinase and Akt(Ser473), decreased platelet spreading on immobilized fibrinogen and inhibited P-selectin expression on platelets. These results demonstrate that LL-37 has antiplatelet and antithrombotic actions.

A Naphthalenic Derivative ND-1 Inhibits Thrombus Formation by Interfering the Binding of Fibrinogen to Integrin αIIbß3.

Integrin αIIbß3 plays a crucial role in the process of platelet aggregation. Three integrin αIIbß3 antagonists (abciximab, eptifibatide, and tirofiban) have been approved by FDA for clinical use. Unfortunately, they all showed severe side effects such as thrombocytopenia and bleeding risk. Thus, researches on the development of more effective and safer antiplatelet agents are needed. In this manuscript we reported a novel naphthalenic derivative compound ND-1 with potent antithrombotic effect and lower bleeding risk. ND-1 inhibited ADP-, collagen-, thrombin-, and U46619-induced platelet aggregation with IC50 values of 1.29, 14.46, 12.84, and 40.24 µM, respectively. Mechanism studies indicated that ND-1 inhibited the binding of fibrinogen to integrin αIIbß3 in a dose-dependent manner with an IC50 value of 3.12 µM. ND-1 inhibited P-selectin expression induced by ADP, collagen, thrombin, and U46619 on the surface of platelets. Additionally, this compound reduced platelets spreading to the immobilized fibrinogen. In vivo, ND-1 potently decreased thrombus formation in an arteriovenous shunt thrombosis model in rats and slightly prolonged bleeding time in a tail cutting model in mice. Taken together, our results reveal that ND-1 is a novel antagonist of αIIbß3 with strong antithrombotic effect and lower bleeding risk.

Synergy Effects of Three Plant Extracts on Protection of Gastric Mucosa.

The gastric mucosa protection effect of three natural plant extracts, Hericium erinaceus (HE), Centella asiatica (CA) and Amomum villosum (AV), were evaluated using the indomethacin damage model. Compared with a single extract, a combination of HE/CA/AV, especially with the ratios of 80:10:10, 45:45:10 and 45:10:45, showed significant synergistic effects for protection of the gastric mucosa with gastric ulcer inhibition rates of 97.8 ± 0.7%, 86.5 ± 2.8% and 86.1 ± 3.6%, respectively. Microscopic appearances of the gastric mucosa were carried out to help confirm the results.