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Catalytic conversion of biomass derivative glucose to high-purity HMF over modified MCM-41 with multiple acid sites in biphasic system.

Background Although the extreme environmental adaptation of organisms is a hot topic in evolutionary biology, genetic adaptation to high-altitude environment remains poorly characterized in ectothermic animals. Squamates are among the most diverse terrestrial vertebrates, with tremendous ecological plasticity and karyotype diversity, and are a unique model system to investigate the genetic footprints of adaptation. Results We report the first chromosome-level assembly of the Mongolian racerunner (Eremias argus) and our comparative genomics analyses found that multiple chromosome fissions/fusions events are unique to lizards. We further sequenced the genomes of 61 Mongolian racerunner individuals that were collected from altitudes ranging from ~ 80 to ~ 2600 m above sea level (m.a.s.l.). Population genomic analyses revealed many novel genomic regions under strong selective sweeps in populations endemic to high altitudes. Genes embedded in those genomic regions are mainly associated with energy metabolism and DNA damage repair pathways. Moreover, we identified and validated two substitutions of PHF14 that may enhance the lizards’ tolerance to hypoxia at high altitudes. Conclusions Our study reveals the molecular mechanism of high-altitude adaptation in ectothermic animal using lizard as a research subject and provides a high-quality lizard genomic resource for future research.

Social sustainability is a major concern of planners and local officials when urban renewal projects are being conducted. Extreme individualism can potentially cause conflicts of interest, making urban renewal in Western cities fraught with various types of social risks. As a country with a deep-rooted socialist tradition, urban renewal projects in China are influenced by collectivist culture and show different features from those of the West. The objective of this research is to investigate how different stakeholders in urban redevelopment projects, including local residents, social organizations, the local state, and developers, interact with each other and how the associated social risks are hedged against. Using a recent well-known project in the city of Guangzhou, the authors attempt to present the latest progress in social risk management in China. With support from a government-sponsored project, the authors have conducted a questionnaire-based survey with a year-long fieldwork follow-up. Using ATLAS.ti software, we found that that “residents’ demand”, “status of collaboration”, and “degree of trust” are the keys to risk management. The results of an ordered probit model show that residents are worried about overall planning, the relocation timetable, and whether their personal needs are taken into account. It is also indicated that the timely disclosure of project information, high-quality public participation, and a reasonable compensation plan can possibly boost the support rate. The authors suggest that utilizing China’s collectivist culture could be an effective way to mitigate social risks, and residents’ personal interests should also be respected.

In vitro maturation (IVM) refers to the process of developing immature oocytes into the mature in vitro under the microenvironment analogous to follicle fluid. It is an important technique for patients with polycystic ovary syndrome and, especially, those young patients with the need of fertility preservation. However, as the mechanisms of oocyte maturation have not been fully understood yet, the cultivation efficiency of IVM is not satisfactory. It was confirmed in our previous study that oocyte maturation was impaired after N-acetyltransferase 10 (NAT10) knockdown (KD). In the present study, we further explored the transcriptome alteration of NAT10-depleted oocytes and found that O-GlcNAcase(OGA) was an important target gene for NAT10-mediated ac4C modification in oocyte maturation. NAT10 might regulate OGA stability and expression by suppressing its degradation. To find out whether the influence of NAT10-mediated ac4C on oocyte maturation was mediated by OGA, we further explored the role of OGA in IVM. After knocking down OGA of oocytes, oocyte maturation was inhibited. In addition, as oocytes matured, OGA expression increased and, conversely, O-linked N-acetylglucosamine (O-GlcNAc) level decreased. On the basis of NAT10 KD transcriptome and OGA KD transcriptome data, NAT10-mediated ac4C modification of OGA might play a role through G protein–coupled receptors, molecular transduction, nucleosome DNA binding, and other mechanisms in oocyte maturation. Rsph6a, Gm7788, Gm41780, Trpc7, Gm29036, and Gm47144 were potential downstream genes. In conclusion, NAT10 maintained the stability of OGA transcript by ac4C modification on it, thus positively regulating IVM. Moreover, our study revealed the regulation mechanisms of oocytes maturation and provided reference for improving IVM outcomes. At the same time, the interaction between mRNA ac4C modification and protein O-GlcNAc modification was found for the first time, which enriched the regulation network of oocyte maturation.

Sulforaphane is the plant active substance with the best anticancer effect and antioxidant found in vegetables. In this paper, based on density functional theory(DFT), the B3LYP/6-311G+(d,p) theoretical level was used to optimize the molecular structure of sulforaphane in gas phase. On the basis of optimization, the first 30 excited states of molecule in methanol were calculated by time-density functional theory(TD-DFT) in SMD solvent model. To analy the excited states of sulforaphane molecule by calculate UV spectrum and hole-electron. Finally, we predicted the active sites of sulforaphane molecule by calculating frontier orbital and fukui function. The results show that: In the UV spectrum, the absorption peaks at 204.4602 and 336.5590nm are the absorption bands of hetero atomic groups of conjugate molecules, which are generated by n-π* transition and belong to R absorption band. According to hole-electron analysis, S0→S18 is the local excitation, and S0→S7, S0→S25 and S0→S29 are the charge transfer excitation. In addition, the O and S atoms on sulfuryl group of sulforaphane are the site of electrophilic reaction; the C and S atoms on the cyanide group are sites of nucleophilic reaction. This study provides a theoretical basis for better understanding the antioxidant and anticancer mechanisms of sulforaphane.

Sika deer are known to prefer oak leaves, which are rich in tannins and toxic to most mammals; however, the genetic mechanisms underlying their unique ability to adapt to living in the jungle are still unclear. In identifying the mechanism responsible for the tolerance of a highly toxic diet, we have made a major advancement in the elucidation of the genomics of sika deer. We generated the first high-quality, chromosome-level genome assembly of sika deer and measured the correlation between tannin intake and RNA expression in 15 tissues through 180 experiments. Comparative genome analyses showed that the UGT and CYP gene families are functionally involved in the adaptation of sika deer to high-tannin food, especially the expansion of UGT genes in a subfamily. The first chromosome-level assembly and genetic characterization of the tolerance toa highly toxic diet suggest that the sika deer genome will serve as an essential resource for understanding evolutionary events and tannin adaptation. Our study provides a paradigm of comparative expressive genomics that can be applied to the study of unique biological features in non-model animals.

There are wide genomic and phenotypic differences between Asian and European pig breeds, yet the current reference genome is the European Duroc pig genome. A high-quality pig genome is lacking for genetic analysis of agricultural traits in Asian pigs. Here, using a hybrid approach, a high-quality reference genome (MSCAAS v1) for the Asian Meishan breed is assembled with a contig N50 size of 48.05 Mb. MSCAAS v1 outperforms the Duroc genome as a reference genome for Asian breeds. Genomic comparison reveals 49,103 structural variations (SVs) between Meishan and Duroc, 4.02% of which are Asian-specific SVs (AP-SVs). Notably, a 30-Mb hotspot for AP-SVs on chromosome X enriched for genes associated with Asian-pig-specific phenotypes is present in Asian domestic pig breeds, but absent in Asian wild boars, suggesting that Asian domestic breeds share a common ancestor. Interbreed transcriptomics reveals transcriptional suppression roles of AP-SVs in multiple tissues. Finally, transcriptional regulation in the intron of IGF2R is reported, as genomic SV (274-bp deletion) in Tibetan pig limits its growth compared to domestic pig breeds. In summary, this study provides insights regarding the genetic changes underlying pig domestication and presents a benchmark-setting resource for the utilization of agricultural valuable loci in Asian pigs.

Few drugs alleviate non-small cell lung cancer (NSCLC) metastasis effectively. Small molecular screening demonstrated that fangchinoline (Fan) reversed epithelial-mesenchymal transition (EMT) in NSCLC cells, inhibiting cell invasion and migration. RNA sequencing (RNA-seq) of Fan-treated NSCLC cells revealed that Fan potently quenched the NADP

The adaptation and diversity of animals to the extreme environments of the Qinghai-Tibet Plateau (QTP) are typical materials to study adaptive evolution. The recently discovered Jinchuan yak population has many individuals with multiple ribs. However, little is known about this yak's origin, evolution, and the genetic mechanisms that formed its unique multirib trait. Here, we report a valuable population genome resource of the Jinchuan yak by resequencing the whole genome of 150 individuals. Population genetic polymorphism and structure analysis reveal that Jinchuan yak can be differentiated as a unique and original yak population among the domestic yak. Combined with geological change, the Jinchuan yak's evolutionary origin is speculated to be about 6290 years ago, which may be related to the unique geographical environment of the eastern edge of the QTP during this period. Compared with other domestic yaks, this new population has 280 positively selected genes. The genes related to skeletal function hold a considerable and remarkable proportion, suggesting that the specific skeletal characteristics have been enhanced in the adaptive evolution of Jinchuan yak in the extreme plateau environment. The genome-wide association study has revealed that TUBA8 and TUBA4A, the genes that regulate the cytoskeleton, are potential genes associated with the multirib trait. Our findings provide a basis to further understand the generation mechanism of the adaptive evolution of this new population in high-altitude extreme environments and the multivertebrate trait of domestic animals.

Gut microbiota dysbiosis is critical in the etiology of polycystic ovary syndrome (PCOS). However, the mechanisms of gut microbiota in PCOS pathogenesis have not been fully elucidated. We aimed to explore the role of gut microbiota-derived macrophage pyroptosis in PCOS. This study conducted dehydroepiandrosterone (DHEA) induced PCOS mice model, 16S rDNA sequencing, western blot, genetic knocking out, transcriptome and translatome profiling, et al. to evaluate the underlying mechanisms. 16S rDNA sequencing showed reduced gut Akkermansia and elevated gram-negative bacteria (Desulfovibrio and Burkholderia) abundances in DHEA induced PCOS mice, which was accompanied by increased serum lipopolysaccharide (LPS). LPS could induce macrophage pyroptosis in mice ovaries, also activated in PCOS. Gasdermin D (GSDMD) is the final executor of macrophage pyroptosis. We demonstrated that Gsdmd knockout in mice could dramatically ameliorate PCOS. Mechanistically, transcriptome and translatome profiling revealed that macrophage pyroptosis disrupted estrogen production and promoted apoptosis of granulosa cells. Interferon (IFN)-γ, which was elevated in PCOS mice serum and ovaries, enhanced macrophage pyroptosis and exacerbated its effect on estrogen receptor in granulosa cells. Inspiringly, we identified that disulfiram and metformin could augment gut Akkermansia abundance, reduce serum IFN-γ level, inhibit macrophage pyroptosis in ovaries, therefore ameliorating PCOS. Collectively, this study emphasizes that macrophage pyroptosis, which was induced by gut microbiota dysbiosis and enhanced by IFN-γ, plays a key role in PCOS pathogenesis through estrogen synthesis dysfunction and apoptosis of granulosa cells. Disulfiram and metformin, which enhanced gut Akkermansia abundance and suppressed macrophage pyroptosis, may be considered as potential therapeutic strategies for PCOS.

The evolutionary direction of gonochorism and hermaphroditism is an intriguing mystery to be solved. The special transient hermaphroditic stage makes the little yellow croaker (Larimichthys polyactis, L. polyactis) an appealing model for studying the formation of hermaphrodites. On the other hand, as the most famous commercial fish species in East Asia, the origin and evolutionary relationship of L. polyactis and Larimichthys crocea remain unclear. Here, we report the genome sequence of L. polyactis, with a size of ~706 Mb (contig N50 = 1.21 Mb and scaffold N50 = 4.52 Mb) and 25,233 protein-coding genes. Phylogenomic analysis suggests that L. polyactis diverged from the common ancestor of Larimichthys crocea ~25.4 million years ago. Our high-quality genome assembly enabled comparative genomic analysis, which revealed a number of within-chromosome rearrangements and translocations without major chromosome fission or fusion events between the two species. The dmrt1 gene was identified as the candidate sex determination gene in L. polyactis. The expression of dmrt1 and its upstream regulatory gene rnf183 were both sexually dimorphic in the transcriptome analysis. Rnf183, unlike its two paralogues rnf223 and rnf225, is only present in Larimichthys but not in other teleost species, suggesting that it originated from a lineage-specific duplication or was lost in other teleosts. Phylogenetic analysis shows that the hermaphrodite stage in male L. polyactis may be explained by the sequence evolution of dmrt1. Decoding the L. polyactis genome not only provides insight into the genetic underpinnings of hermaphrodite evolution but also provides valuable information for enhancing fish aquaculture.

N4-acetylcytidine (ac4C), a newly identified epigenetic modification within mRNA, has been characterized as a crucial regulator of mRNA stability and translation efficiency. However, the role of ac4C during oocyte maturation, the process mainly controlled via post-transcriptional mechanisms, has not been explored. N-acetyltransferase 10 (NAT10) is the only known enzyme responsible for ac4C production in mammals and ac4C-binding proteins have not been reported yet. In this study, we have documented decreasing trends of both ac4C and NAT10 expression from immature to mature mouse oocytes. With NAT10 knockdown mediated by small interfering RNA (siRNA) in germinal vesicle (GV)-stage oocytes, ac4C modification was reduced and meiotic maturation in vitro was significantly retarded. Specifically, the rate of first polar body extrusion was significantly decreased with NAT10 knockdown (34.6%) compared to control oocytes without transfection (74.6%) and oocytes transfected with negative control siRNA (72.6%) (p < 0.001), while rates of germinal vesicle breakdown (GVBD) were not significantly different (p = 0.6531). RNA immunoprecipitation and high-throughput sequencing using HEK293T cells revealed that the modulated genes were enriched in biological processes associated with nucleosome assembly, chromatin silencing, chromatin modification and cytoskeletal anchoring. In addition, we identified TBL3 as a potential ac4C-binding protein by a bioinformatics algorithm and RNA pulldown with HEK293T cells, which may mediate downstream cellular activities. Taken together, our results suggest that NAT10-mediated ac4C modification is an important regulatory factor during oocyte maturation in vitro and TBL3 is a potential ac4C-binding protein.

The Arctic fox (Vulpes lagopus) is the only fox species occurring in the Arctic and has adapted to its extreme climatic conditions. Currently, the molecular basis of its adaptation to the extreme climate has not been characterized. Here, we applied PacBio sequencing and chromosome structure capture technique to assemble the first V. lagopus genome assembly, which is assembled into chromosome fragments. The genome assembly has a total length of 2.345 Gb with a contig N50 of 31.848 Mb and a scaffold N50 of 131.537 Mb, consisting of 25 pseudochromosomal scaffolds. The V. lagopus genome had approximately 32.33% repeat sequences. In total, 21,278 protein-coding genes were predicted, of which 99.14% were functionally annotated. Compared with 12 other mammals, V. lagopus was most closely related to V. Vulpes with an estimated divergence time of ~7.1 Ma. The expanded gene families and positively selected genes potentially play roles in the adaptation of V. lagopus to Arctic extreme environment. This high-quality assembled genome will not only promote future studies of genetic diversity and evolution in foxes and other canids but also provide important resources for conservation of Arctic species.

Dietary fiber intake is associated with a low incidence of suffering from metabolic syndrome. To explore the potential health benefits of walnut meal dietary fiber (WMDF) as a prebiotic, the functional role of WMDF on metabolic syndrome in mice induced by high fructose diet (20%, HF) was investigated. The animal experiment results showed that administration of WMDF to HF-fed mice alleviated abnormal body weight gain, insulin resistance, oxidative stress, lipid metabolism disorders and inflammation. Histopathological observation confirmed the preventative effects of WMDF on hepatic steatosis and vascular endothelial dysfunction. Also, WMDF intake increased the production of acetic acid, propionic acid and butyric acid. Moreover, WMDF ingestion effectively improved the disorder of gut microbiota caused by HF, increased the diversity of gut microbiota and the relative abundance of short-chain fatty acids-producing bacteria. These findings demonstrate WMDF can be used as a prebiotic to prevent HF-induced metabolic syndrome.

Extant giant pandas are divided into Sichuan and Qinling subspecies. The giant panda has many species-specific characteristics, including comparatively small organs for body size, small genitalia of male individuals, and low reproduction. Here, we report the most contiguous, high-quality chromosome-level genomes of two extant giant panda subspecies to date, with the first genome assembly of the Qinling subspecies. Compared with the previously assembled giant panda genomes based on short reads, our two assembled genomes increased contiguity over 200-fold at the contig level. Additional sequencing of 25 individuals dated the divergence of the Sichuan and Qinling subspecies into two distinct clusters from 10,000 to 12,000 years ago. Comparative genomic analyses identified the loss of regulatory elements in the dachshund family transcription factor 2 (DACH2) gene and specific changes in the synaptotagmin 6 (SYT6) gene, which may be responsible for the reduced fertility of the giant panda. Positive selection analysis between the two subspecies indicated that the reproduction-associated IQ motif containing D (IQCD) gene may at least partly explain the different reproduction rates of the two subspecies. Furthermore, several genes in the Hippo pathway exhibited signs of rapid evolution with giant panda-specific variants and divergent regulatory elements, which may contribute to the reduced inner organ sizes of the giant panda.

The acute thermal response has been extensively studied in commercial chickens because of the adverse effects of heat stress on poultry production worldwide. Here, we performed whole-genome resequencing of autochthonous Niya chicken breed native to the Taklimakan Desert region as well as of 11 native chicken breeds that are widely distributed and reared under native humid and temperate areas. We used combined statistical analysis to search for putative genes that might be related to the adaptation of hot arid and harsh environment in Niya chickens. We obtained a list of intersected candidate genes with log2 θπ ratio, FST and XP-CLR (including 123 regions of 21 chromosomes with the average length of 54.4 kb) involved in different molecular processes and pathways implied complex genetic mechanisms of adaptation of native chickens to hot arid and harsh environments. We identified several selective regions containing genes that were associated with the circulatory system and blood vessel development (BVES, SMYD1, IL18, PDGFRA, NRP1, and CORIN), related to central nervous system development (SIM2 and NALCN), related to apoptosis (CLPTM1L, APP, CRADD, and PARK2) responded to stimuli (AHR, ESRRG FAS, and UBE4B) and involved in fatty acid metabolism (FABP1). Our findings provided the genomic evidence of the complex genetic mechanisms of adaptation to hot arid and harsh environments in chickens. These results may improve our understanding of thermal, drought, and harsh environment acclimation in chickens and may serve as a valuable resource for developing new biotechnological tools to breed stress-tolerant chicken lines and or breeds in the future.

Summary Decades of artificial selection have significantly improved performance and efficiency of animal production systems. However, little is known about the microevolution of genomes due to intensive breeding. Using whole-genome sequencing, we document dynamic changes of chicken genomes under divergent selection on adiposity over 19 generations. Directional selection reduced within-line but increased between-line genomic differences. We observed that artificial selection tended to result in recruitment of preexisting variations of genes related to adipose tissue growth. In addition, novel mutations contributed to divergence of phenotypes under selection but contributed significantly less than preexisting genomic variants. Integration of 15 generations genome sequencing, genome-wide association study, and multi-omics data further identified that genes involved in signaling pathways important to adipogenesis, such as autophagy and lysosome (URI1, MBL2), neural system (CHAT), and endocrine (PCSK1) pathways, were under strong selection. Our study provides insights into the microevolutionary dynamics of domestic animal genomes under artificial selection., Graphical Abstract, Highlights • Directional selection reduces within-line but increases between-line genomic difference • Artificial selection tends to recruit preexisting variations of genes for fatness • Novel mutations contribute to the divergence of fatness under artificial selection • Genes involved in signaling pathways important to adipogenesis are under selection, Biological Sciences; Evolutionary Biology; Genetics; Genomics

Our paper analyzes full plastid DNA sequence data of 202 wild and cultivated diploid potatoes, Solanum section Petota, to explore its phylogenetic utility compared to prior analyses of the same accessions using genome-wide nuclear SNPs, and plastid DNA restriction site data. The present plastid analysis discovered the same major clades as the nuclear data but with some substantial differences in topology within the clades. The considerably larger plastid and nuclear data sets add phylogenetic resolution within the prior plastid DNA restriction site data, highlight plastid/nuclear incongruence that supports hypotheses of hybridization/introgression to help explain the taxonomic difficulty in the section.

Animal genomes in the Qinghai-Tibetan Plateau provide valuable resources for scientists to understand the molecular mechanism of environmental adaptation. Tibetan fish species play essential roles in the local ecology; however, the genomic information for native fishes was still insufficient. Oxygymnocypris stewartii, belonging to Oxygymnocypris genus, Schizothoracinae subfamily, is a native fish in the Tibetan plateau living within the elevation from roughly 3,000 m to 4,200 m. In this report, PacBio and Illumina sequencing platform were used to generate ~385.3 Gb genomic sequencing data. A genome of about 1,849.2 Mb was obtained with a contig N50 length of 257.1 kb. More than 44.5% of the genome were identified as repetitive elements, and 46,400 protein-coding genes were annotated in the genome. The assembled genome can be used as a reference for future population genetic studies of O. stewartii and will improve our understanding of high altitude adaptation of fishes in the Qinghai-Tibetan Plateau.

Nitric oxide (NO), a widespread signaling transduction molecule in organism, plays key roles in lots of pathophysiological processes. Aberrant level of NO is closely related to tumors, cardiovascular and cerebrovascular diseases, neurodegenerative diseases and many other diseases. Therefore, sensing NO in cells and in vivo is of great significance for the study of the chemical biology of related diseases. Herein, a novel ratiometric fluorescence probe (AC-SA), in which anthracene carboximide used as fluorophore and secondary amines at the 6th position of the fluorophore severed as recognition moiety is rationally designed to detect NO. The AC-SA can capture NO via N-nitrosation reaction to give obvious fluorescence signal change from red to green based on the intramolecular charge transfer (ICT) mechanism. The AC-SA features striking ratiometric signal (I525/I625), good sensitivity (4.05 nM), high selectivity for sensing NO over various interferents in physiological pH. More important, the AC-SA can be applied to image endogenous NO in Raw 264.7 macrophage cells as well as zebrafish in a ratiometric manner.

In this work, we have developed a new carbazole-based fluorescent probe (E)-1-methyl-4-(2-(5-(9-phenyl-9H-carbazol-3-yl) thiophen-2-yl)vinyl)pyridin-1-ium (PCTP) for ratiometric and colormetric ClO− sensing. PCTP displayed red emission due to the intramolecular charge transfer (ICT) effect of phenylcarbazol moiety, while this effect can be rapidly weakened and led to the significant fluorescence change (from red to green) in the presence of ClO−. PCTP is more highly selective and sensitive towards ClO− detection than other various biological related species. The detection limit (LOD) was calculated to be 10.8 nM. More importantly, PCTP has been successfully applied in ClO− imaging in living cells and zebrafishes.

Background Mechanisms for high-altitude adaption have attracted widespread interest among evolutionary biologists. Several genome-wide studies have been carried out for endemic vertebrates in Tibet, including mammals, birds, and amphibians. However, little information is available about the adaptive evolution of highland fishes. Glyptosternon maculatum (Regan 1905), also known as Regan or barkley and endemic to the Tibetan Plateau, belongs to the Sisoridae family, order Siluriformes (catfishes). This species lives at an elevation ranging from roughly 2,800 m to 4,200 m. Hence, a high-quality reference genome of G. maculatum provides an opportunity to investigate high-altitude adaption mechanisms of fishes. Findings To obtain a high-quality reference genome sequence of G. maculatum, we combined Pacific Bioscience single-molecule real-time sequencing, Illumina paired-end sequencing, 10X Genomics linked-reads, and BioNano optical map techniques. In total, 603.99 Gb sequencing data were generated. The assembled genome was about 662.34 Mb with scaffold and contig N50 sizes of 20.90 Mb and 993.67 kb, respectively, which captured 83% complete and 3.9% partial vertebrate Benchmarking Universal Single-Copy Orthologs. Repetitive elements account for 35.88% of the genome, and 22,066 protein-coding genes were predicted from the genome, of which 91.7% have been functionally annotated. Conclusions We present the first comprehensive de novo genome of G. maculatum. This genetic resource is fundamental for investigating the origin of G. maculatum and will improve our understanding of high-altitude adaption of fishes. The assembled genome can also be used as reference for future population genetic studies of G. maculatum.

In a recent issue of PNAS, Hardigan et al. (1) state that the genetic diversity of the potato is much greater than that of other major crops, based on 68.9 million SNPs identified from the resequencing of 67 accessions of wild and cultivated potatoes. We questioned this conclusion based on our own original analysis of wild and cultivated potato species (2) and estimates of genomic SNPs in other major crops by next-generation resequencing with a few to 15 million SNPs. Examples include soybean (3), pigeon pea (4), cotton (5), tomato (6), and potato (2) (Table 1). To explore this further, we reanalyzed the raw data from ref. 1 using standard, stricter methods to filter SNPs … [↵][1]1To whom correspondence may be addressed. Email: binquan.huang{at}plants.ox.ac.uk, David.Spooner{at}ars.usda.gov, or liangqiqi{at}novogene.com. [1]: #xref-corresp-1-1

Wild potato species have substantial phenotypic and physiological diversity. Here, we report a comprehensive assessment of wild and cultivated potato species based on genomic analyses of 201 accessions of Solanum section Petota . We sequenced the genomes of these 201 accessions and identified 6 487 006 high-quality single nucleotide polymorphisms (SNPs) from 167 accessions in clade 4 of Solanum section Petota , including 146 wild and 21 cultivated diploid potato accessions with a broad geographic distribution. Genome-wide genetic variation analysis showed that the diversity of wild potatoes is higher than that of cultivated potatoes, and much higher genetic diversity in the agronomically important disease resistance genes was observed in wild potatoes. Furthermore, by exploiting information about known quantitative trait loci (QTL), we identified 609 genes under selection, including those correlated with the loss of bitterness in tubers and those involved in tuberization, two major domesticated traits of potato. Phylogenetic analyses revealed a north-south division of all species in clade 4, not just those in the S. brevicaule complex, and further supported S. candolleanum as the progenitor of cultivated potato and the monophyletic origin of cultivated potato in southern Peru. In addition, we analyzed the genome of S. candolleanum and identified 529 genes lost in cultivated potato. Collectively, the molecular markers generated in this study provide a valuable resource for the identification of agronomically important genes useful for potato breeding.

Stabilized Fe-Mn binary oxide nanoparticles were synthesized and tested for removal and in-situ immobilization of Se(IV) in groundwater and soil. A water-soluble starch or food-grade carboxymethyl cellulose (CMC) was used as a stabilizer to facilitate in-situ delivery of the particles into contaminated soil. While bare and stabilized nanoparticles showed rapid sorption kinetics, starch-stabilized Fe-Mn offered the greatest capacity for Se(IV). The Langmuir maximum capacity was determined to be 109 and 95 mg-Se/g-Fe for starch- and CMC-stabilized nanoparticles, respectively, and the high Se(IV) uptake was observed over the typical groundwater pH range of 5-8. Column breakthrough tests indicated that the stabilized nanoparticles were deliverable in a model sandy soil while non-stabilized particles were not. When a Se(IV)-spiked soil was treated in situ with the nanoparticles, >90% water leachable Se(IV) was transferred to the nanoparticle phase, and thereby immobilized as the particles were retained in the downstream soil matrix. The nanoparticle amendment reduced the TCLP (toxicity characteristic leaching procedure) leachability and the California WET (waste extraction test) leachability of Se(IV) by 76% and 71%, respectively. The technology holds the potential to fill a major technology gap in remediation of metals-contaminated soil and groundwater.

This study investigated effectiveness of starch-stabilized magnetite nanoparticles for in situ enhanced sorption and immobilization of arsenate, As(V), in a model sandy loam soil. Batch tests showed that the nanoparticles offered an As(V) distribution coefficient of 10,000 L/g, which is >3 orders of magnitude greater than that for the soil. Batch and column experimental results revealed that the nanoparticle treatment greatly reduced water-leachable As(V) and the leachability of As(V) remaining in the soil per TCLP (Toxicity Characteristic Leaching Procedure) analysis. Column tests showed that water-leachable As(V) from the As(V)-laden soil containing 31.45 mg/kg was reduced by ∼93% and the TCLP leachability by >83% when the soil was treated with 34 pore volumes of a 0.1 g-Fe/L of the nanoparticle suspension. While the nanoparticles are deliverable in the soil, the effective travel distance of the nanoparticles can be manipulated by controlling the injection flow rate. Under natural groundwater flow conditions (velocity ≤2.4 × 10 −4 cm/s), the delivered nanoparticles are confined within a limited distance (

Magnetite nanoparticles were synthesized with starch and sodium carboxymethyl cellulose (CMC) as a stabilizer, and tested for enhanced arsenate removal. Starch at ≥0.04 wt % or CMC at ≥0.005 wt % stabilized 0.1 g/L (as Fe) of the nanoparticles. While CMC-stabilized magnetite displays a highly negative zeta (ζ) potential, starch-stabilized magnetite shows a nearly neutral surface. Increasing the starch concentration from 0 to 0.04 wt % doubles the arsenate uptake, yet the nanoparticles remain settleable by gravity. Further increasing the starch concentration to 0.1 wt % results in fully dispersed nanoparticles and increases the arsenate uptake by 14%. Starch-stabilized magnetite offers a much faster sorption rate and greater capacity than CMC-stabilized magnetite. The sorption kinetics can be modeled using an intraparticle-diffusion model. The sorption capacity increases with decreasing pH. Dissolved organic matter at 20 mg/L as TOC decreases the arsenate uptake by 19.1%. When aged for >1.5 years, the nano...

Gossypium hirsutum contributes the most production of cotton fibre, but G. barbadense is valued for its better comprehensive resistance and superior fibre properties. However, the allotetraploid genome of G. barbadense has not been comprehensively analysed. Here we present a high-quality assembly of the 2.57 gigabase genome of G. barbadense, including 80,876 protein-coding genes. The double-sized genome of the A (or At) (1.50 Gb) against D (or Dt) (853 Mb) primarily resulted from the expansion of Gypsy elements, including Peabody and Retrosat2 subclades in the Del clade and the Athila subclade in the Athila/Tat clade. Substantial gene expansion and contraction were observed and rich homoeologous gene pairs with biased expression patterns were identified, suggesting abundant gene sub-functionalization occurred by allopolyploidization. More specifically, the CesA gene family has adapted differentially temporal expression patterns, suggesting an integrated regulatory mechanism of CesA genes from At and Dt subgenomes for the primary and secondary cellulose biosynthesis of cotton fibre in a “relay race”-like fashion. We anticipate that the G. barbadense genome sequence will advance our understanding the mechanism of genome polyploidization and underpin genome-wide comparison research in this genus.

Ion exchange (IX) is considered by US EPA as one of the best available technologies for removing arsenic from drinking water. However, typical IX processes will generate large volumes of arsenic-laden regenerant brine that requires costly further handling and disposal. This study aimed to develop an engineered strategy to minimize the production and arsenic leachability of the process waste residual. We prepared and tested a new class of starch-bridged magnetite nanoparticles for removal of arsenate from spent IX brine. A low-cost, "green" starch at 0.049% (w/w) was used as a stabilizer to prevent the nanoparticles from agglomerating and as a bridging agent allowing the nanoparticles to flocculate and precipitate while maintaining their high arsenic sorption capacity. When applied to a simulated spent IX brine containing 300 mg/L As and 6% (w/w) NaCl, nearly 100% removal of arsenic was achieved within 1 h using the starch-bridged nanoparticles at an Fe-to-As molar ratio of 7.6, compared to only 20% removal when bare magnetite particles were used. Increasing NaCl in the brine from 0 to 10% (w/w) had little effect on the arsenic sorption capacity. Maximum uptake was observed within a pH range of 4-6. The Langmuir capacity coefficient was determined to be 248 mg/g at pH 5.0. The final treatment sludge was able to pass the TCLP (Toxicity Characteristic Leaching Procedure) based leachability of 5 mg/L as As.

Magnetite nanoparticles were synthesized in the presence of polysaccharides and tested for enhanced arsenate removal. The nanoparticles were characterized and tested with respect to sorption of As(III) and As(V) from water and for immobilization in soil. Polysaccharide-modified magnetite nanoparticles offer a much higher As sorption capacity compared with that offered by their nonstabilized counterparts. The polysaccharide-to-iron ratio can be altered to yield nanoparticles of various properties. One of the potential uses of the starch-bridged magnetite nanoparticles is to remove As from spent ion exchange brine and provide easy separation from water by gravity. Stabilized magnetite nanoparticles are readily deliverable to soils, and the spent particles would be retained under normal groundwater conditions. The nanoparticle amendment provides an environmentally friendly and cost-effective way to comply with the newly enforced maximum contaminant level of 10 μg/L.