Variations and reduction of plastome are associated with the evolution of parasitism in Convolvulaceae

Parasitic lifestyle can often relax the constraint on the plastome, leading to gene pseudogenization and loss, and resulting in diverse genomic structures and rampant genome degradation. Although several plastomes of parasitic Cuscuta have  been reported, the evolution of parasitism in the family Convolvulaceae which is linked to structural variations and reduction of plastome has not been well investigated. In this study, we assembled and collected 40 plastid genomes belonging to 23 species representing four subgenera of Cuscuta and ten species of autotrophic Convolvulaceae. Our findings revealed nine types of structural variations and six types of inverted repeat (IR) boundary variations in the plastome of Convolvulaceae spp. These structural variations were associated with the shift of parasitic lifestyle, and IR boundary shift, as well as the abundance of long repeats. Overall, the degradation of Cuscuta plastome proceeded gradually, with one clade exhibiting an accelerated degradation rate. We observed five stages of gene loss in Cuscuta, including NAD(P)H complex → PEP complex → Photosynthesis-related → Ribosomal protein subunits → ATP synthase complex. Based on our results, we speculated that the shift of parasitic lifestyle in early divergent time promoted relaxed selection on plastomes, leading to the accumulation of microvariations, which ultimately resulted in the plastome reduction. This study provides new evidence towards a better understanding of plastomic evolution, variation, and reduction in the genus Cuscuta.

Comparative analyses of mitogenomes in the social bees with insights into evolution of long inverted repeats in the Meliponini

The insect mitogenome is typically a compact circular molecule with highly conserved gene contents. Nonetheless, mitogenome structural variations have been reported in specific taxa, and gene rearrangements, usually the tRNAs, occur in different lineages. Because synapomorphies of mitogenome organizations can provide information for phylogenetic inferences, comparative analyses of mitogenomes have been given increasing attention. However, most studies use a very few species to represent the whole genus, tribe, family, or even order, overlooking potential variations at lower taxonomic levels, which might lead to some incorrect inferences. To provide new insights into mitogenome organizations and their implications for phylogenetic inference, this study conducted comparative analyses for mitogenomes of three social bee tribes (Meliponini, Bombini, and Apini) based on the phylogenetic framework with denser taxonomic sampling at the species and population levels. Comparative analyses revealed that mitogenomes of Apini and Bombini are the typical type, while those of Meliponini show diverse variations in mitogenome sizes and organizations. Large inverted repeats (IRs) cause significant gene rearrangements of protein coding genes (PCGs) and rRNAs in Indo-Malay/Australian stingless bee species. Molecular evolution analyses showed that the lineage with IRs have lower d N/ d S ratios for PCGs than lineages without IRs, indicating potential effects of IRs on the evolution of mitochondrial genes. The finding of IRs and different patterns of gene rearrangements suggested that Meliponini is a hotspot in mitogenome evolution. Unlike conserved PCGs and rRNAs whose rearrangements were found only in the mentioned lineages within Meliponini, tRNA rearrangements are common across all three tribes of social bees, and are significant even at the species level, indicating that comprehensive sampling is needed to fully understand the patterns of tRNA rearrangements, and their implications for phylogenetic inference.

Comparative analyses of eight complete plastid genomes of two hemiparasitic Cassytha vines in the family Lauraceae

Cassytha is the sole genus of hemiparasitic vines (ca. 20 spp.) belonging to the Cassytheae tribe of the Lauraceae family. It is extensively distributed in tropical and subtropical regions. In this study, we determined the complete plastid genome sequences of C. filiformis and C. larsenii, which do not possess the typical quadripartite structure. The length of C. filiformis plastomes ranged from 114,215 to 114,618 bp, whereas that of C. larsenii plastomes ranged from 114,900 to 114,988 bp. Comparative genomic analysis revealed 1,013 mutation sites, four large intragenomic deletions, and five highly variable regions in the eight plastome sequences. Phylogenetic analyses based on 61 complete plastomes of Laurales species, 19 ITS sequences, and trnK barcodes from 91 individuals of Cassytha spp. confirmed a non-basal group comprising individuals of C. filiformis, C. larsenii, and C. pubescens in the family Lauraceae and proposed a sister relationship between C. filiformis and C. larsenii. Further morphological comparisons indicated that the presence or absence of hairs on the haustoria and the shape or size of fruits were useful traits for differentiating C. filiformis and C. larsenii.

Fibroblast growth factor 15, induced by elevated bile acids, mediates the improvement of hepatic glucose metabolism after sleeve gastrectomy

BACKGROUND

Fibroblast growth factor (FGF) 15/19, which is expressed in and secreted from the distal ileum, can regulate hepatic glucose metabolism in an endocrine manner. The levels of both bile acids (BAs) and FGF15/19 are elevated after bariatric surgery. However, it is unclear whether the increase in FGF15/19 is induced by BAs. Moreover, it remains to be understood whether FGF15/19 elevations contribute to improvements in hepatic glucose metabolism after bariatric surgery.

AIM

To investigate the mechanism of improvement of hepatic glucose metabolism by elevated BAs after sleeve gastrectomy (SG).

METHODS

By calculating and comparing the changes of body weight after SG with SHAM group, we examined the weight-loss effect of SG. The oral glucose tolerance test (OGTT) test and area under the curve of OGTT curves were used to assess the anti-diabetic effects of SG. By detecting the glycogen content, expression and activity of glycogen synthase as well as the glucose-6-phosphatase (G6Pase) and phosphoenolpyruvate carboxykinase (Pepck), we evaluated the hepatic glycogen content and gluconeogenesis activity. We examined the levels of total BA (TBA) together with the farnesoid X receptor (FXR)-agonistic BA subspecies in systemic serum and portal vein at week 12 post-surgery. Then the histological expression of ileal FXR and FGF15 and hepatic FGF receptor 4 (FGFR4) with its corresponding signal pathways involved in glucose metabolism were detected.

RESULTS

After surgery, food intake and body weight gain of SG group was decreased compare with the SHAM group. The hepatic glycogen content and glycogen synthase activity was significantly stimulated after SG, while the expression of the key enzyme for hepatic gluconeogenesis: G6Pase and Pepck, were depressed. TBA levels in serum and portal vein were both elevated after SG, the FXR-agonistic BA subspecies: Chenodeoxycholic acid (CDCA), lithocholic acid (LCA) in serum and CDCA, DCA, LCA in portal vein were all higher in SG group than that in SHAM group. Consequently, the ileal expression of FXR and FGF15 were also advanced in SG group. Moreover, the hepatic expression of FGFR4 was stimulated in SG-operated rats. As a result, the activity of its corresponding pathway for glycogen synthesis: FGFR4-Ras-extracellular signal regulated kinase pathway was stimulated, while the corresponding pathway for hepatic gluconeogenesis: FGFR4- cAMP regulatory element-binding protein- peroxisome proliferator-activated receptor γ coactivator-1α pathway was suppressed.

CONCLUSION

Elevated BAs after SG induced FGF15 expression in distal ileum by activating their receptor FXR. Furthermore, the promoted FGF15 partly mediated the improving effects on hepatic glucose metabolism of SG.

Mitochondrial genome sequencing and analysis of the invasive Microstegium vimineum: a resource for systematics, invasion history, and management

Premise of the Research

Plants remain underrepresented among species with sequenced mitochondrial genomes (mitogenomes), due to the difficulty in assembly with short-read technology. Invasive species lag behind crops and other economically important species in this respect, representing a lack of tools for management and land conservation efforts.

Methodology

The mitogenome of Microstegium vimineum, one of the most damaging invasive plant species in North America, was sequenced and analyzed using long-read data, providing a resource for biologists and managers. We conducted analyses of genome content, phylogenomic analyses among grasses and relatives based on mitochondrial coding regions, and an analysis of mitochondrial single nucleotide polymorphism in this invasive grass species.

Pivotal Results

The assembly is 478,010 bp in length and characterized by two large, inverted repeats, and a large, direct repeat. However, the genome could not be circularized, arguing against a "master circle" structure. Long-read assemblies with data subsets revealed several alternative genomic conformations, predominantly associated with large repeats. Plastid-like sequences comprise 2.4% of the genome, with further evidence of Class I and Class II transposable element-like sequences. Phylogenetic analysis placed M. vimineum with other Microstegium species, excluding M. nudum, but with weak support. Analysis of polymorphic sites across 112 accessions of M. vimineum from the native and invasive ranges revealed a complex invasion history.

Conclusions

We present an in-depth analysis of mitogenome structure, content, phylogenetic relationships, and range-wide genomic variation in M. vimineum's invasive US range. The mitogenome of M. vimineum is typical of other andropogonoid grasses, yet mitochondrial sequence variation across the invasive and native ranges is extensive. Our findings suggest multiple introductions to the US over the last century, with subsequent spread, secondary contact, long-distance dispersal, and possibly post-invasion selection on awn phenotypes. Efforts to produce genomic resources for invasive species, including sequenced mitochondrial genomes, will continue to provide tools for their effective management, and to help predict and prevent future invasions.

Duodenal-jejunal bypass increases intraduodenal bile acids and upregulates duodenal SIRT1 expression in high-fat diet and streptozotocin-induced diabetic rats

BACKGROUND

The mechanisms underlying diabetes remission after duodenal-jejunal bypass (DJB) remain elusive. In DJB surgery, the duodenum is excluded. However, the duodenum has emerged as an important regulator of glucose homeostasis, and elevated duodenal SIRT1 leads to improved hepatic insulin sensitivity. After DJB, bile acids (BAs) in the duodenum are not mixed and diluted by the ingested food. And activation of BA receptors promotes SIRT1 expression in many tissues. We hypothesized that BA-mediated upregulation of SIRT1 may contribute to diabetic control after DJB.

AIM

To investigate the surgical effects of DJB on duodenal SIRT1 expression and uncover the potential crosslinks between BAs and SIRT1.

METHODS

Twenty diabetic rats were randomly allocated to the sham (n = 10) and DJB (n = 10) groups. Body weight, food intake, fasting blood glucose (FBG), serum and intraduodenal total BA (TBA) levels were measured accordingly. Oral glucose tolerance test (OGTT) and intraperitoneal pyruvate tolerance test (ipPTT) were performed to evaluate the effects of surgeries on systemic glucose disposal and hepatic gluconeogenesis. The key genes of BA signaling pathway in the duodenal mucosa, including farnesoid X receptor (FXR), small heterodimer partner (SHP), and Takeda G-protein-coupled receptor 5 (TGR5) were evaluated by real-time quantitative polymerase chain reaction 8 wk postoperatively. The duodenal SIRT1, AMPK, and phosphorylated AMPK (p-AMPK) levels were evaluated by western blotting. Rat small intestine epithelial IEC-6 cells were treated with GW4064 and INT-777 to verify the effects of BAs on SIRT1 expression in enterocytes.

RESULTS

The DJB group exhibited body weight and food intake comparable to those of the sham group at all postoperative time points. The FBG level and area under the curve for the OGTT and ipPTT were significantly lower in the DJB group. The DJB group exhibited higher fasting and postprandial serum TBA levels than the sham group at both 2 and 8 wk postoperatively. At 8 wk after surgery, the DJB group showed higher intraluminal TBA concentration, upregulated mRNA expression of FXR and SHP, and elevated protein expression of SIRT1 and p-AMPK in the descending and horizontal segments of the duodenum. Activation of FXR and TGR5 receptors by GW4064 and INT-777 increased the mRNA and protein expression of SIRT1 and promoted the phosphorylation of AMPK in IEC-6 cells.

CONCLUSION

DJB elevates intraduodenal BA levels and activates the duodenal BA signaling pathway, which may upregulate duodenal SIRT1 and further contribute to improved glucose homeostasis after DJB.

The complete chloroplast genomes of two Pedicularis species (Orobanchaceae) from Southwest China

We report the complete chloroplast genome (plastome) sequences of Pedicularis cephalantha (147,087 bp) and P. nigra (145,726 bp), endemic to southwestern China. Both plastomes have typical quadripartite structures with one large-single copy region, one small-single copy region, and two inverted repeat regions. Both plastome sequences contained 37 tRNA genes and eight rRNA genes, but they differed in the numbers of protein-coding genes: P. cephalantha had 76 functional genes and 12 pseudogenes while P. nigra had 74 functional genes and 13 pseudogenes. Phylogenetic analysis shows that P. cephalantha and P. nigra are closely related, then sister to P. oederi in the family Orobanchaceae.

Increasing Taxa Sampling Provides New Insights on the Phylogenetic Relationship Between Eriobotrya and Rhaphiolepis

Eriobotrya (Rosaceae) is an economically important genus with around 30 species. It is widely distributed in tropical and warm temperate regions of Asia, with most of its species in China, Myanmar, and Vietnam. However, Eriobotrya is often confused with the smaller genus Rhaphiolepis, and the phylogenetic relationships between the two genera are controversial. Here we present phylogenetic analyses of 38 newly generated Eriobotrya and Rhaphiolepis nrDNA together with 16 sequences of nrDNA and 28 sequences of ITS obtained from GenBank, representing 28 species of Eriobotrya and 12 species of Rhaphiolepis, in order to reconstruct highly supported relationships for the two genera. Contrary to previous research based on limited sampling, our results highlight the monophyly of Eriobotrya as well as Rhaphiolepis. The topology recovered here is consistent with key morphological synapomorphies such as the persistent sepals in Eriobotrya. Our findings show that increased sampling of taxa can provide a more robust phylogeny through reducing phylogenetic error and increasing overall phylogenetic accuracy.

Cryptic Species Diversification of the Pedicularis siphonantha Complex (Orobanchaceae) in the Mountains of Southwest China Since the Pliocene

Morphological approaches often fail to delimit species in recently derived species complexes. This can be exacerbated in historical collections which may have lost key features in specimen preparation and preservation. Here, we examine the Pedicularis siphonantha complex, endemic to the Mountains of Southwest China. This complex is characterized by its red/purple/pink and long-tubular corolla, and twisted, beaked galea. However, herbarium specimens are often difficult to identify to species. Molecular approaches using nrITS or nuclear ribosomal internal transcribed spacer (nrITS) + plastid DNA (ptDNA) have been successfully used for species identification in Pedicularis. To resolve taxonomic confusion in the Pedicularis siphonantha complex, we reconstructed phylogenies of the complex using nrITS and four plastid DNA loci (matK, rbcL, trnH-psbA, and trnL-F). To recover as much of the phylogenetic history as possible, we sampled individuals at the population level. Topological incongruence between the nrITS and ptDNA datasets was recovered in clades including two widely distributed species, Pedicularis milliana and Pedicularis tenuituba. Based on morphological, geographical, and genetic evidence, we suggest that hybridization/introgression has occurred between P. milliana and Pedicularis sigmoidea/Pedicularis sp. 1 in the Yulong Snow Mountain of Lijiang, northwest Yunnan, and between P. tenuituba and Pedicularis leptosiphon in Ninglang, northwest Yunnan. After removing conflicting DNA regions in Pedicularis dolichosiphon (nrITS) and P. milliana (ptDNA), the concatenated nrITS and ptDNA phylogenies distinguish 11 species in the P. siphonantha complex, including two undescribed species, from the Jiaozi and Yulong Snow Mountains, respectively. Phylogeographical analyses indicate that the P. siponantha complex originated from south of the Hengduan Mountains, expanding north to the Himalayas and the Yunnan-Guizhou Plateau. Moreover, the uplift of the Qinghai-Tibet Plateau and climate oscillations may have driven further diversification in the complex.

Plastid phylogenomic insights into relationships of all flowering plant families

BACKGROUND

Flowering plants (angiosperms) are dominant components of global terrestrial ecosystems, but phylogenetic relationships at the familial level and above remain only partially resolved, greatly impeding our full understanding of their evolution and early diversification. The plastome, typically mapped as a circular genome, has been the most important molecular data source for plant phylogeny reconstruction for decades.

RESULTS

Here, we assembled by far the largest plastid dataset of angiosperms, composed of 80 genes from 4792 plastomes of 4660 species in 2024 genera representing all currently recognized families. Our phylogenetic tree (PPA II) is essentially congruent with those of previous plastid phylogenomic analyses but generally provides greater clade support. In the PPA II tree, 75% of nodes at or above the ordinal level and 78% at or above the familial level were resolved with high bootstrap support (BP ≥ 90). We obtained strong support for many interordinal and interfamilial relationships that were poorly resolved previously within the core eudicots, such as Dilleniales, Saxifragales, and Vitales being resolved as successive sisters to the remaining rosids, and Santalales, Berberidopsidales, and Caryophyllales as successive sisters to the asterids. However, the placement of magnoliids, although resolved as sister to all other Mesangiospermae, is not well supported and disagrees with topologies inferred from nuclear data. Relationships among the five major clades of Mesangiospermae remain intractable despite increased sampling, probably due to an ancient rapid radiation.

CONCLUSIONS

We provide the most comprehensive dataset of plastomes to date and a well-resolved phylogenetic tree, which together provide a strong foundation for future evolutionary studies of flowering plants.

Characteristics of the complete chloroplast genome sequences of Stylidium debile and Stylidium petiolare (Stylidiaceae)

We report complete chloroplast genome (plastome) sequences of Stylidium debile (150,105 bp) and Stylidium petiolare (150,998 bp). Both plastomes had the typical quadripartite structure, with large single-copy (LSC) and small single-copy (SSC) regions separated by two inverted repeat (IR) regions. Both plastomes have lost the rps19 and ycf15 CDS genes, and had infA-like, rps22-like, and rps7-like pseudogenes. Moreover, IR regions were expanded by having trnH ^GUG tRNA and the rps22-like pseudogene. Plastome phylogenomic analyses showed that the two Stylidium species formed a monophyletic clade (BS = 100), sister to the Argophyllaceae (BS = 86/83). Sequence differences between the two Stylidium plastomes were 5011 sites, including 2166 variable sites and 2845 indels, with the petA-psbJ spacer the most variable region, followed by the trnK ^UUU-matK intron and trnG ^UUG-rps16 spacer.

Plastid NDH Pseudogenization and Gene Loss in a Recently Derived Lineage from the Largest Hemiparasitic Plant Genus Pedicularis (Orobanchaceae)

The plastid genome (plastome) is highly conserved in both gene order and content and has a lower mutation rate than the nuclear genome. However, the plastome is more variable in heterotrophic plants. To date, most such studies have investigated just a few species or only holoheterotrophic groups, and few have examined plastome evolution in recently derived lineages at an early stage of transition from autotrophy to heterotrophy. In this study, we investigated the evolutionary dynamics of plastomes in the monophyletic and recently derived Pedicularis sect. Cyathophora (Orobanchaceae). We obtained 22 new plastomes, 13 from the six recognized species of section Cyathophora, six from hemiparasitic relatives and three from autotrophic relatives. Comparative analyses of gene content, plastome structure and selection pressure showed dramatic differences among species in section Cyathophora and in Pedicularis as a whole. In comparison with autotrophic relatives and other Pedicularis spp., we found that the inverted repeat (IR) region in section Cyathophora had expansions to the small single-copy region, with a large expansion event and two independent contraction events. Moreover, NA(D)H dehydrogenase, accD and ccsA have lost function multiple times, with the function of accD being replaced by nuclear copies of an accD-like gene in Pedicularis spp. The ccsA and ndhG genes may have evolved under selection in association with IR expansion/contraction events. This study is the first to report high plastome variation in a recently derived lineage of hemiparasitic plants and therefore provides evidence for plastome evolution in the transition from autotrophy to heterotrophy.

Four new species and a new record of Orchidinae (Orchidaceae: Orchideae) from China

Four new species of Orchidaceae from China, Heminium lijiangense, Peristylus fasciculatus, Platanthera milinensis, and Ponerorchis gongshanensis, together with a new country record, Peristylus tenuicallus, are described and illustrated based on morphological and/or phylogenetic analyses. Heminium lijiangense is closely related to H. elisabethae but differs from it by having the dorsal sepal ovate-orbicular and lip mid-lobe distinctly shorter than lateral lobes. P. fasciculatus is close to Peristylus tradescantifolius but is distinguished from it by having several fascicled and straight, root-like tubers (vs. one or two oblongoid tubers), old stems usually persistent, middle lobe of lip narrowly ligulate-lanceolate and half as long as the lateral lobes (vs. middle lobe deltoid, about a third as long as the lateral lobes or less), a raised callus at the base of each lateral lobe (vs. callus absent), spur gradually attenuate toward the apex (vs. spur clavate). Platanthera milinensis is similar to P. stenochila by sharing small green flowers and lip without a spur, but differs in having a creeping rhizome, a corymbose inflorescence, and a broadly ovate and slightly 3-lobed lip. Ponerochis gongshanensis is similar to P. faberi in its small flowers, but differs in having a linear leaf c. 3 mm wide (vs. leaf 5-13 mm wide), in the lip having collar-like raised margins on the sides of the spur entrance, and a mid-lobe which is notched at the apex but not divided into two divergent lobules that are nearly as large as the lateral lobes, as in P. faberi. All the proposed species obtained high support in phylogenetic analysis as new species. The recently described genus Apetalanthe is reduced to synonymy of Ponerorchis and a new combination is made.

Three new species of Liparis s.l. (Orchidaceae: Malaxideae) from Southwest China based on morphological characters and phylogenetic evidence

Liparis aureolabella and L. mengziensis, two new species from the karst region of southwestern China, and L. bingzhongluoensis, a new species from montane region in Yunnan, are described and illustrated. L. aureolabella is easily distinguished from its relatives by having abaxially purple leave with purple reticulate veins prominent adaxially, a lip auriculate at base, and falcate-lanceolate pollinia. Liparis mengziensis is closely related to L. petiolata and L. auriculata, but differs from them by having an ovate to broadly ovate leaf, purple lip and apex connate along the margins. Liparis bingzhongluoensis is similar to Liparis nanlingensis, but the new species is characterized by having a lip with two transparent ridges on its disc, longitudinally concave basal callus and triangular column wings. Phylogenetic analyses based on nuclear ribosomal ITS and plastid matK sequences showed that L. aureolabella and L. mengziensis are nested with L. petiolata or L. auriculata in a monophyletic clade. L. bingzhongluoensis is sister to a clade formed by L. nanlingensis, L. tsii, L. sasakii and L. krameri. Moreover, morphological comparisons strongly support that the three species as separated species newly to science.

Genomic evidence of prevalent hybridization throughout the evolutionary history of the fig-wasp pollination mutualism

Ficus (figs) and their agaonid wasp pollinators present an ecologically important mutualism that also provides a rich comparative system for studying functional co-diversification throughout its coevolutionary history (~75 million years). We obtained entire nuclear, mitochondrial, and chloroplast genomes for 15 species representing all major clades of Ficus. Multiple analyses of these genomic data suggest that hybridization events have occurred throughout Ficus evolutionary history. Furthermore, cophylogenetic reconciliation analyses detect significant incongruence among all nuclear, chloroplast, and mitochondrial-based phylogenies, none of which correspond with any published phylogenies of the associated pollinator wasps. These findings are most consistent with frequent host-switching by the pollinators, leading to fig hybridization, even between distantly related clades. Here, we suggest that these pollinator host-switches and fig hybridization events are a dominant feature of fig/wasp coevolutionary history, and by generating novel genomic combinations in the figs have likely contributed to the remarkable diversity exhibited by this mutualism.

Complete plastome sequence of Aspidopterys obcordata (Malpighiaceae), a traditional Dai medicinal plant from Xishuangbanna, Yunnan, China

We reported the first complete plastid genome of Aspidopterys (Malpighiaceae) in this study. The complete plastome of Aspidopterys obcordata is 160,453 bp in length with a base composition of A (31.4%), G (18.5%), C (18.2%), and T (32.0%). Structurally, the genome contains two short inverted repeats (26,905 bp for each), which are separated by a large single copy region (88,491 bp) and a small single copy region (18,152 bp). The plastome contained 113 unique genes, including 79 protein-coding genes, 30 transfer RNAs, and 4 ribosomal RNAs. Phylogenetic analyses showed that A. obcordata was sister to Bunchosia argentea in the monophyletic Malpighiaceae. This study provided a high-quality plastome sequence for future studies in Aspidopterys, as well as Malpighiaceae.

GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes

GetOrganelle is a state-of-the-art toolkit to accurately assemble organelle genomes from whole genome sequencing data. It recruits organelle-associated reads using a modified "baiting and iterative mapping" approach, conducts de novo assembly, filters and disentangles the assembly graph, and produces all possible configurations of circular organelle genomes. For 50 published plant datasets, we are able to reassemble the circular plastomes from 47 datasets using GetOrganelle. GetOrganelle assemblies are more accurate than published and/or NOVOPlasty-reassembled plastomes as assessed by mapping. We also assemble complete mitochondrial genomes using GetOrganelle. GetOrganelle is freely released under a GPL-3 license ( https://github.com/Kinggerm/GetOrganelle ).

GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes

GetOrganelle is a state-of-the-art toolkit to accurately assemble organelle genomes from whole genome sequencing data. It recruits organelle-associated reads using a modified "baiting and iterative mapping" approach, conducts de novo assembly, filters and disentangles the assembly graph, and produces all possible configurations of circular organelle genomes. For 50 published plant datasets, we are able to reassemble the circular plastomes from 47 datasets using GetOrganelle. GetOrganelle assemblies are more accurate than published and/or NOVOPlasty-reassembled plastomes as assessed by mapping. We also assemble complete mitochondrial genomes using GetOrganelle. GetOrganelle is freely released under a GPL-3 license ( https://github.com/Kinggerm/GetOrganelle ).

The complete mitochondrial genome sequence of Lactarius trivialis (Russulalles, Basidiomycota)

Lactarius trivialis is a very common species and widely distributes in north temperate. In this study, a complete mitogenome of L. trivialis was assembled and annotated. The whole mitogenome of L. trivialis was a circular molecule with 42,366 bp in length, encoding 44 genes as follows: 19 coding genes, two rRNAs, and 23 tRNAs. The contents of four bases in mtDNA were A (39.65%), T (38.82%), C (11.30%), and G (21.53%), respectively. Phylogenetic analysis recovered that it is nested with other Lactarius spp. in the order Russulalles.

Decoding the evolution and transmissions of the novel pneumonia coronavirus (SARS-CoV-2 / HCoV-19) using whole genomic data

The outbreak of COVID-19 started in mid-December 2019 in Wuhan, China. Up to 29 February 2020, SARS-CoV-2 (HCoV-19 / 2019-nCoV) had infected more than 85 000 people in the world. In this study, we used 93 complete genomes of SARS-CoV-2 from the GISAID EpiFlu ^TM database to investigate the evolution and human-to-human transmissions of SARS-CoV-2 in the first two months of the outbreak. We constructed haplotypes of the SARS-CoV-2 genomes, performed phylogenomic analyses and estimated the potential population size changes of the virus. The date of population expansion was calculated based on the expansion parameter tau ( τ) using the formula t= τ/2 u. A total of 120 substitution sites with 119 codons, including 79 non-synonymous and 40 synonymous substitutions, were found in eight coding-regions in the SARS-CoV-2 genomes. Forty non-synonymous substitutions are potentially associated with virus adaptation. No combinations were detected. The 58 haplotypes (31 found in samples from China and 31 from outside China) were identified in 93 viral genomes under study and could be classified into five groups. By applying the reported bat coronavirus genome (bat-RaTG13-CoV) as the outgroup, we found that haplotypes H13 and H38 might be considered as ancestral haplotypes, and later H1 was derived from the intermediate haplotype H3. The population size of the SARS-CoV-2 was estimated to have undergone a recent expansion on 06 January 2020, and an early expansion on 08 December 2019. Furthermore, phyloepidemiologic approaches have recovered specific directions of human-to-human transmissions and the potential sources for international infected cases.

Decoding the evolution and transmissions of the novel pneumonia coronavirus (SARS-CoV-2 / HCoV-19) using whole genomic data

The outbreak of COVID-19 started in mid-December 2019 in Wuhan, China. Up to 29 February 2020, SARS-CoV-2 (HCoV-19 / 2019-nCoV) had infected more than 85 000 people in the world. In this study, we used 93 complete genomes of SARS-CoV-2 from the GISAID EpiFlu TM database to investigate the evolution and human-to-human transmissions of SARS-CoV-2 in the first two months of the outbreak. We constructed haplotypes of the SARS-CoV-2 genomes, performed phylogenomic analyses and estimated the potential population size changes of the virus. The date of population expansion was calculated based on the expansion parameter tau ( τ) using the formula t= τ/2 u. A total of 120 substitution sites with 119 codons, including 79 non-synonymous and 40 synonymous substitutions, were found in eight coding-regions in the SARS-CoV-2 genomes. Forty non-synonymous substitutions are potentially associated with virus adaptation. No combinations were detected. The 58 haplotypes (31 found in samples from China and 31 from outside China) were identified in 93 viral genomes under study and could be classified into five groups. By applying the reported bat coronavirus genome (bat-RaTG13-CoV) as the outgroup, we found that haplotypes H13 and H38 might be considered as ancestral haplotypes, and later H1 was derived from the intermediate haplotype H3. The population size of the SARS-CoV-2 was estimated to have undergone a recent expansion on 06 January 2020, and an early expansion on 08 December 2019. Furthermore, phyloepidemiologic approaches have recovered specific directions of human-to-human transmissions and the potential sources for international infected cases.

Leveraging plastomes for comparative analysis and phylogenomic inference within Scutellarioideae (Lamiaceae)

Scutellaria, or skullcaps, are medicinally important herbs in China, India, Japan, and elsewhere. Though Scutellaria is the second largest and one of the more taxonomically challenging genera within Lamiaceae, few molecular systematic studies have been undertaken within the genus; in part due to a paucity of available informative markers. The lack of informative molecular markers for Scutellaria hinders our ability to accurately and robustly reconstruct phylogenetic relationships, which hampers our understanding of the diversity, phylogeny, and evolutionary history of this cosmopolitan genus. Comparative analyses of 15 plastomes, representing 14 species of subfamily Scutellarioideae, indicate that plastomes within Scutellarioideae contain about 151,000 nucleotides, and possess a typical quadripartite structure. In total, 590 simple sequence repeats, 489 longer repeats, and 16 hyper-variable regions were identified from the 15 plastomes. Phylogenetic relationships among the 14 species representing four of the five genera of Scutellarioideae were resolved with high support values, but the current infrageneric classification of Scutellaria was not supported in all analyses. Complete plastome sequences provide better resolution at an interspecific level than using few to several plastid markers in phylogenetic reconstruction. The data presented here will serve as a foundation to facilitate DNA barcoding, species identification, and systematic research within Scutellaria, which is an important medicinal plant resource worldwide.

De novo assembling a complete mitochondrial genome of Pedicularis rex (Orobanchaceae) using GetOrganelle toolkit

We reported the first mitogenome of Pedicularis from P. rex (Orobanchaceae), which is endemic to SW China. The complete mitochondrial genome (mitogenome or chondriome) was a single circular chromosome that was 219,859 bp in length. It contains 56 genes, including 34 protein-coding (cox2 and atp9 with two copies), 19 transfer RNA (tRNA), and three ribosomal RNA (rRNA) genes. Phylogenetic analysis showed that Pedicularis rex was closely related to Castilleja paramensis.

Complete plastome sequence of Acorus tatarinowii (Acoraceae), a traditional Chinese medicinal plant from Xishuangbanna, Yunnan, China

The complete plastome of Acorus tatarinowii is 153,296 bp in length, with two long inverted repeats (25,752 bp for each) separating by a large single-copy (83,533 bp) and a small single-copy (18,240 bp). The plastome contained 112 unique genes, including 78 protein-coding genes, 30 transfer RNAs, and 4 ribosomal RNAs. Phylogenetic analyses showed that A. tatarinowii was closely related to A. gramineus.

[The value of multi-gene testing in benign or malign diagnosis of thyroid nodules with indeterminate cytology]

Objective: To study the diagnostic value of a multi-gene molecular testing in cytologically indeterminate thyroid nodules. Methods: From February 2018 to September 2018, patients with thyroid nodules who underwent fine needle aspiration(FNA) at Peking University Cancer Hospital were enrolled. Three hundred and sixty patients were included, consisting of 86 men and 274 women, with a mean age of 45.8 years (between 13 and 89 years old). Among 391 nodules, 141 were cytologically inderminate and 75 were resected. FNA samples underwent prospective testing using a next-generation sequencing (NGS) assay, which included 16 genes for point mutations and 26 types of gene fusions. The testing results of indeterminate nodules were compared with surgical outcomes, to determine the diagnostic performance. The results were compared with the BRAF V600E single gene mutation analysis by χ(2) test. Results: The multi-gene testing showed a sensitivity of 73.2%, specificity of 96.8%, positive predictive value of 96.8%, and negative predictive value of 73.2%. The diagnostic accuracy of multi-gene testing was significantly higher than the BRAF V600E mutation test (83.3% vs 73.6%, χ(2)=31.588, P<0.01). Conclusion: Multi-gene testing in FNA samples is an effective method to diagnose cytologically indeterminate thyroid nodules, which has a higher accuracy than BRAF V600E mutation detection.

Convergent horizontal gene transfer and cross-talk of mobile nucleic acids in parasitic plants

Horizontal gene transfer (HGT), the movement and genomic integration of DNA across species boundaries, is commonly associated with bacteria and other microorganisms, but functional HGT (fHGT) is increasingly being recognized in heterotrophic parasitic plants that obtain their nutrients and water from their host plants through direct haustorial feeding. Here, in the holoparasitic stem parasite Cuscuta, we identify 108 transcribed and probably functional HGT events in Cuscuta campestris and related species, plus 42 additional regions with host-derived transposon, pseudogene and non-coding sequences. Surprisingly, 18 Cuscuta fHGTs were acquired from the same gene families by independent HGT events in Orobanchaceae parasites, and the majority are highly expressed in the haustorial feeding structures in both lineages. Convergent retention and expression of HGT sequences suggests an adaptive role for specific additional genes in parasite biology. Between 16 and 20 of the transcribed HGT events are inferred as ancestral in Cuscuta based on transcriptome sequences from species across the phylogenetic range of the genus, implicating fHGT in the successful radiation of Cuscuta parasites. Genome sequencing of C. campestris supports transfer of genomic DNA-rather than retroprocessed RNA-as the mechanism of fHGT. Many of the C. campestris genes horizontally acquired are also frequent sources of 24-nucleotide small RNAs that are typically associated with RNA-directed DNA methylation. One HGT encoding a leucine-rich repeat protein kinase overlaps with a microRNA that has been shown to regulate host gene expression, suggesting that HGT-derived parasite small RNAs may function in the parasite-host interaction. This study enriches our understanding of HGT by describing a parasite-host system with unprecedented gene exchange that points to convergent evolution of HGT events and the functional importance of horizontally transferred coding and non-coding sequences.

China's biodiversity hotspots revisited: A treasure chest for plants

n/a.

Gentianella macrosperma, a new species of Gentianella (Gentianaceae) from Xinjiang, China

Gentianella macrosperma Ma ex H.F. Cao, J.D. Ya & Q.R. Zhang, a new species of Gentianaceae from Xinjiang, Northwest China is described and illustrated. This new species is unique in having equal length of corolla lobe and corolla tube, nectaries located at the throat of the corolla tube and large seeds up to 1.6 mm in diameter. In addition, an updated identification key to the Chinese species of Gentianella is provided.

Taxonomic and nomenclatural notes on Pedicularis (Orobanchaceae): I. One new species from northwest Yunnan, China

Pedicularis multicaulis W.B.Yu, H.Wang & D.Z.Li (series Oliganthae Prain) is a new species described and illustrated herein. This new species is endemic to northwest Yunnan and only two populations were found in Weixi county. Phylogenetic analyses support P. multicaulis as a new species, sister to P. taihaiensis Bonati and P. macilenta Franch. Morphological comparisons between P. multicaulis and P. macilenta and P. taihaiensis also support P. multicaulis as a new species to science.

A Direct Current Measurement Method Based on Terbium Gallium Garnet Crystal and a Double Correlation Detection Algorithm

When applying an optical current transformer (OCT) to direct current measurement, output signals exhibit a low signal-to-noise ratio and signal-to-noise band overlap. Sinusoidal wave modulation is used to solve this problem. A double correlation detection algorithm is used to extract the direct current (DC) signal, remove white noise and improve the signal-to-noise ratio. Our sensing unit uses a terbium gallium garnet crystal in order to increase the output signal-to-noise ratio and measurement sensitivity. Measurement errors of single correlation and double correlation detection algorithms are compared, and experimental results showed that this measurement method can control measurement error to about 0.3%, thus verifying its feasibility.

[Fine-needle aspiration for the diagnosis of lymph node metastasis in papillary thyroid carcinoma]

Objective: To investigate the diagnostic performance of fine-needle aspiration (FNA) cytology for the detection of lateral lymph node metastases in patients with papillary thyroid carcinoma (PTC). Methods: A total of 109 lateral lymph nodes with suspicious metastases from 85 patients were retrospectively subjected to FNAC, fine-needle aspiration thyroglobulin measurement (FNATg), and FNATg/SerumTg measurement. Lymph node pathological results after surgery were taken as the gold standard. Using Mann-Whitney U test, Pearson linear model and ROC curve were used for data analysis. Results: The sensitivity, specificity and accuracy of FNATg for the diagnosis of lateral neck lymph node metastasis were respectively 93.7%, 90.0% and 93.3% and those of FNATg/SerumTg were respectively 89.9%, 90.0% and 93.2% respectively, the threshold values for FNATg and FNATg/SerumTg were 0.925 ng/ml and 1.007, respectively. The sensitivity, specificity and accuracy of FNATg combined with FNAC were respectively 91.0%,93.5% and 94.4%. The existence of thyroid tissue and the expression of serum Tg did not affect the expression of lymph node FNATg. The FNATg cutoff value of 0.925 ng/ml showed the best diagnostic performance in patients with a thyroid gland, while the FNATg/SerumTg cutoff ratio of 14.95 showed the best diagnostic performance in patients without a thyroid gland. The serum TgAb significantly interfered with the expression of FNATg in the lateral neck metastatic lymph nodes (P=0.049). Conclusions: FNATg alone or the combination of FNATg with FNAC are highly reliable in the diagnosis of lateral neck lymph node metastases in patients with PTC. The expression of TgAb may interfere with the accuracy of the diagnostic performance of FNATg.

Risk factors and score for recollapse of the augmented vertebrae after percutaneous vertebroplasty in osteoporotic vertebral compression fractures

Our study demonstrated a high incidence of recollapse of the augmented vertebrae after PVP treatment for OVCFs. A risk score based on all significant factors can predict the rate of recollapse and gain clinical benefits to prevent recollapse in patients at high risk.

BACKGROUND

Recollapse of the augmented vertebrae after percutaneous vertebroplasty (PVP) treatment for osteoporotic vertebral compression fractures (OVCFs) has obtained much attention. However, little is known about risk factors and score for recollapse of the augmented vertebrae.

OBJECTIVE

To determine risk factors and furthermore develop a risk score related to recollapse of the augmented vertebrae after PVP treatment for OVCFs.

METHODS

Patients who were treated with PVP for single OVCFs and met this study's inclusion criteria were retrospectively reviewed. The follow-up period was at least 2 years. Associations of recollapse with co-variates (age, gender, bone mass density [BMD] with a T-score, fracture level, intravertebral cleft [IVC], fracture type, cement volume, cement leakage, leakage into a disc, cement distribution pattern, Non-PMMA-endplate-contact [NPEC], preoperative fracture severity, reduction rate [RR], reduction angle [RA]) were analyzed and a risk score for recollapse was further developed to predict recollapse.

RESULTS

A total of 152 patients were included. Recollapse group was found in 42 (27.6%) patients. Preoperative IVC, solid lump cement distribution pattern, more RR (a cutoff value of 7%) and larger RA (a cutoff value of 3°) was significantly associated with increased risk for recollapse of the augmented vertebrae. A risk score was developed based on the number of risk factors present in each patient. Patients with a score of 4 had an approximately ninefold increased risk of developing recollapse over patients with a score of 0. The receiver operating characteristic curve of the risk score generated an area under the curve of 0.899 (95% CI 0.642-0.836, P = 0.000).

CONCLUSION

A risk score based on preoperative IVC, cement distribution pattern, reduction rate, and reduction angle predicts the rate of recollapse. Additional studies should aim to validate this score and inspect clinical benefits of recollapse prophylaxis in patients at high risk.

Phylogenetic approaches resolve taxonomical confusion in Pedicularis (Orobanchaceae): Reinstatement of Pedicularis delavayi and discovering a new species Pedicularis milliana

Morphological identification of Pedicularis depends on floral characters. However, some important characters may be lost during the process of pressing the specimen. Pedicularis delavayi was described from northwestern Yunnan, and widely adopted as a variety of P. siphonantha. Unfortunately, the name "P. siphonantha var. delavayi' incorrectly referred to P. milliana (a new species described in this study) or P. tenuituba in some herbarium specimens and publications. Moreover, phylogenetic relationships among P. delavayi, P. siphonantha and its allies (P. milliana and P. tenuituba) were not fully resolved. In this study, we sampled 76 individuals representing 56 taxa. Of them, 10 taxa were from P. siphonantha lineage, and 11 individuals of P. delavayi represented 9 populations. These species were named as P. siphonantha group on the basis of morphological similarity. Nuclear ribosomal internal transcribed spacer (nrITS) and four chloroplast genes/regions were used for phylogenetic analyses. Phylogenetic analyses showed that the P. siphonantha group was polyphyletic: P. delavayi was sister to P. obliquigaleata in clade A; and the remaining species of P. siphonantha group were monophyletic in clade B, named as P. siphonantha lineage. In the P. siphonantha lineage, P. milliana, P. siphonantha, and P. tenuituba were well supported as monophyletic, and P. dolichosiphon was sister to P. leptosiphon. Morphologically, P. delavayi differs from species of the P. siphonantha lineage in having a long petiole (~ 50 mm) and pedicel (~ 40 mm), a ridged corolla tube, and a folded lower-lip of the corolla. Therefore, both morphological characters and phylogenetic evidence strongly supported to reinstate P. delavayi as an independent species and describe P. milliana as new species. In addition, P. neolatituba was proposed to reduce as a new synonymy of P. delavayi.

Evolutionary Comparisons of the Chloroplast Genome in Lauraceae and Insights into Loss Events in the Magnoliids

Available plastomes of the Lauraceae show similar structure and varied size, but there has been no systematic comparison across the family. In order to understand the variation in plastome size and structure in the Lauraceae and related families of magnoliids, we here compare 47 plastomes, 15 newly sequenced, from 27 representative genera. We reveal that the two shortest plastomes are in the parasitic Lauraceae genus Cassytha, with lengths of 114,623 (C. filiformis) and 114,963 bp (C. capillaris), and that they have lost NADH dehydrogenase (ndh) genes in the large single-copy region and one entire copy of the inverted repeat (IR) region. The plastomes of the core Lauraceae group, with lengths from 150,749 bp (Nectandra angustifolia) to 152,739 bp (Actinodaphne trichocarpa), have lost trnI-CAU, rpl23, rpl2, a fragment of ycf2, and their intergenic regions in IRb region, whereas the plastomes of the basal Lauraceae group, with lengths from 157,577 bp (Eusideroxylon zwageri) to 158,530 bp (Beilschmiedia tungfangensis), have lost rpl2 in IRa region. The plastomes of Calycanthus (Calycanthaceae, Laurales) have lost rpl2 in IRb region, but the plastome of Caryodaphnopsis henryi (Lauraceae) remain intact, as do those of the nonLaurales magnoliid genera Piper, Liriodendron, and Magnolia. On the basis of our phylogenetic analysis and structural comparisons, different loss events occurred in different lineages of the Laurales, and fragment loss events in the IR regions have largely driven the contraction of the plastome in the Lauraceae. These results provide new insights into the evolution of the Lauraceae as well as the magnoliids as a whole.

Downregulation of histone demethylase JMJD1C inhibits colorectal cancer metastasis through targeting ATF2

Colorectal cancer (CRC) is one of the most common malignant gastrointestinal cancers. Metastasis is a major leading of death in patients with CRC and many patients have metastatic disease at diagnosis. However, the underlying molecular mechanisms are still elusive. Here, we showed that JMJD1C was overexpressed in colon cancer tissues compared to normal samples and was positively associated with metastasis and poor prognosis. Silencing JMJD1C strongly inhibits CRC migration and invasion both in vitro and in vivo. Further, we found that knockdown of JMJD1C decreased the protein and mRNA levels of ATF2, mechanistically, and JMJD1C regulated the expression of ATF2 by modulating the H3K9me2 but not H3K9me1 activity. In addition, we further performed some "rescues experiments". We found that overexpression of ATF2 could reverse the abrogated migration and invasion ability by knockdown of JMJD1C in CRC. Our results demonstrated that an increase of JMJD1C was observed in colon cancer and knockdown of JMJD1C regulated CRC metastasis by inactivation of the ATF2 pathway. This novel JMJD1C/ATF2 signaling pathway may be a promising therapeutic target for CRC metastasis.

Low-pressure pneumoperitoneum with abdominal wall lift in laparoscopic total mesorectal excision for rectal cancer: Initial experience

AIM

To evaluate the safety and feasibility of a new technology combining low-pressure pneumoperitoneum (LPP) and abdominal wall lift (AWL) in laparoscopic total mesorectal excision (TME) for rectal cancer.

METHODS

From November 2015 to July 2017, 26 patients underwent laparoscopic TME for rectal cancer using LPP (6-8 mmHg) with subcutaneous AWL in Qilu Hospital of Shandong University, Jinan, China. Clinical data regarding patients’ demographics, intraoperative monitoring indices, operation-related indices and pathological outcomes were prospectively collected.

RESULTS

Laparoscopic TME was performed in 26 cases (14 anterior resection and 12 abdominoperineal resection) successfully, without conversion to open or laparoscopic surgery with standard-pressure pneumoperitoneum. Intraoperative monitoring showed stable heart rate, blood pressure and paw airway pressure. The mean operative time was 194.29 ± 41.27 min (range: 125-270 min) and 200.41 ± 20.56 min (range: 170-230 min) for anterior resection and abdominoperineal resection, respectively. The mean number of lymph nodes harvested was 16.71 ± 5.06 (range: 7-27). There was no positive circumferential or distal resection margin. No local recurrence was observed during a median follow-up period of 11.96 ± 5.55 mo (range: 5-23 mo).

CONCLUSION

LPP combined with AWL is safe and feasible for laparoscopic TME. The technique can provide satisfactory exposure of the operative field and stable operative monitoring indices.

The Hemiparasitic Plant Phtheirospermum (Orobanchaceae) Is Polyphyletic and Contains Cryptic Species in the Hengduan Mountains of Southwest China

Phtheirospermum (Orobanchaceae), a hemiparasitic genus of Eastern Asia, is characterized by having long and viscous glandular hairs on stems and leaves. Despite this unifying character, previous phylogenetic analyses indicate that Phtheirospermum is polyphyletic, with Phtheirospermum japonicum allied with tribe Pedicularideae and members of the Ph. tenuisectum complex allied with members of tribe Rhinantheae. However, no analyses to date have included broad phylogenetic sampling necessary to test the monophyly of Phtheirospermum species, and to place these species into the existing subfamiliar taxonomic organization of Orobanchaceae. Two other genera of uncertain phylogenetic placement are Brandisia and Pterygiella, also both of Eastern Asia. In this study, broadly sampled phylogenetic analyses of nrITS and plastid DNA revealed hard incongruence between these datasets in the placement of Brandisia. However, both nrITS and the plastid datasets supported the placement of Ph. japonicum within tribe Pedicularideae, and a separate clade consisting of the Ph. tenuisectum complex and a monophyletic Pterygiella. Analyses were largely in agreement that Pterygiella, the Ptheirospermum complex, and Xizangia form a clade not nested within any of the monophyletic tribes of Orobanchaceae recognized to date. Ph. japonicum, a model species for parasitic plant research, is widely distributed in Eastern Asia. Despite this broad distribution, both nrITS and plastid DNA regions from a wide sampling of this species showed high genetic identity, suggesting that the wide species range is likely due to a recent population expansion. The Ph. tenuisectum complex is mainly distributed in the Hengduan Mountains region. Two cryptic species were identified by both phylogenetic analyses and morphological characters. Relationships among species of the Ph. tenuisectum complex and Pterygiella remain uncertain. Estimated divergence ages of the Ph. tenuisectum complex corresponding to the last two uplifts of the Qinghai-Tibet Plateau at around 8.0-7.0 Mya and 3.6-1.5 Mya indicated that the development of a hot-dry valley climate during these uplifts may have driven species diversification in the Ph. tenuisectum complex.

Geometry-dependent band shift and dielectric modification of nanoporous Si nanowires

In order to obtain a detailed understanding of the modulation of electronic properties in nanoporous Si (np-Si) nanowires with containing ordered, nanometer-sized cylindrical pores, we propose a theoretical method to clarify the band shift and associated with the dielectric modification determined by the geometrical parameters, including nanowire diameter, pore size, pore spacing and porosity, in terms of size-dependent surface energy and atomic-bond-relaxation correlation mechanism. Our results reveal that the self-equilibrium strain induced by the atoms located at inner and outer surfaces with high ratio of under-coordinated atoms as well as elastic interaction among pores in np-Si nanowires play the dominant role in the bandgap shift and dielectric depression. The tunable electronic properties of np-Si nanowires with negative curvature make them attractive for nanoelectronic and optoelectronic devices.

[Hypoxia regulates the expression of OPG/RANKL mRNA in rat bone marrow mesenchymal stem cells]

PURPOSE

To investigate the effects of hypoxia on the expression of osteoprotegerin (OPG) and receptor activator of nuclear factor kappa B ligand (RANKL) mRNA in rat bone marrow mesenchymal stem cells (rBMSCs).

METHODS

rBMSCs were isolated and cultured by whole bone marrow cell adherent method, and an optimal hypoxic preconditioning model was established with CoCl₂ (cobalt chloride). rBMSCs were incubated in cell culture mediums with different concentrations of CoCl₂ (final concentrations of CoCl₂ were 0, 50, 100, 200, 400 μmol/L) and incubated for different times. MTT assay was applied to detect the effect of CoCl₂ on cell proliferation. mRNA and protein expression of HIF-1α of rBMSCs was detected by real-time PCR and Western blot. After treated with 100 μmol/L CoCl₂ for 0, 12, 24, 48, 72, 96 h, the expression of rBMSCs OPG/RANKL mRNA were detected by real-time PCR. The differences in distribution of each genotype were analyzed with SPSS 18.0 software package.

RESULTS

Compared with the control group, 200, 400 μmol/L CoCl₂ inhibited the proliferation of rBMSCs (P<0.05). However, 50, 100 μmol/L CoCl₂ had no significant impact on the proliferation of rBMSCs (P>0.05). Real-time PCR and Western blot showed that HIF-1α expression in 50 μmol/L and 100 μmol/L CoCl₂ groups was significantly higher than the control group; the effect of 100 μmol/L CoCl₂ was significantly greater than 50 μmol/L CoCl₂. After cultivated in hypoxia condition for 12 h, the expression of OPG and RANKL mRNA in rBMSCs didn't change significantly (P>0.05). After cultured hypoxia condition for 24, 48, 72, 96 h, the expression of OPG mRNA in rBMSCs increased while the RANKL decreased, thus the ratio of OPG/RANKL increased and the difference was significant (P<0.05).

CONCLUSIONS

Hypoxia can regulate the mRNA expression of OPG and RANKL mRNA in rBMSCs and significantly promote osteogenic differentiation.

Phylogenetic reassessment of tribe Anemoneae (Ranunculaceae): Non-monophyly of Anemone s.l. revealed by plastid datasets

Morphological and molecular evidence strongly supported the monophyly of tribe Anemoneae DC.; however, phylogenetic relationships among genera of this tribe have still not been fully resolved. In this study, we sampled 120 specimens representing 82 taxa of tribe Anemoneae. One nuclear ribosomal internal transcribed spacer (nrITS) and six plastid markers (atpB-rbcL, matK, psbA-trnQ, rpoB-trnC, rbcL and rps16) were amplified and sequenced. Both Maximum likelihood and Bayesian inference methods were used to reconstruct phylogenies for this tribe. Individual datasets supported all traditional genera as monophyletic, except Anemone and Clematis that were polyphyletic and paraphyletic, respectively, and revealed that the seven single-gene datasets can be split into two groups, i.e. nrITS + atpB-rbcL and the remaining five plastid markers. The combined nrITS + atpB-rbcL dataset recovered monophyly of subtribes Anemoninae (i.e. Anemone s.l.) and Clematidinae (including Anemoclema), respectively. However, the concatenated plastid dataset showed that one group of subtribes Anemoninae (Hepatica and Anemone spp. from subgenus Anemonidium) close to the clade Clematis s.l. + Anemoclema. Our results strongly supported a close relationship between Anemoclema and Clematis s.l., which included Archiclematis and Naravelia. Non-monophyly of Anemone s.l. using the plastid dataset indicates to revise as two genera, new Anemone s.l. (including Pulsatilla, Barneoudia, Oreithales and Knowltonia), Hepatica (corresponding to Anemone subgenus Anemonidium).

Establishment of polyethylene-glycol-mediated protoplast transformation for Lecanicillium lecanii and development of virulence-enhanced strains against Aphis gossypii

BACKGROUND

Lecanicillium lecanii has been developed as a biopesticide and used in biological control of several agricultural insects. To improve fungal virulence, an optimised polyethylene glycol (PEG)-mediated protoplast transformation system was established for L. lecanii. Pr1A-like cuticle-degrading protease gene (Cdep1) from Beauveria bassiana was transferred into L. lecanii, and its resulting activity against Aphis gossypii was assessed.

RESULTS

The optimised protoplast generation yielded 2.5 × 10(8) protoplasts g(-1) wet mycelium of fungi, and gave nearly 98% viability and 80% regeneration on plates. Protease activities were increased about fivefold in transformants expressing CDEP1. The median lethal concentration (LC50 ) for transformants expressing CDEP1 was twofold lower than that for the wild type (WT). The median survival time (LT50 ) for transformants expressing CDEP1 was also 14.2% shorter than that for WT, though no significant difference. There were no significant differences in conidial germination as colony growth and conidial yield on plates between transformants expressing CDEP1 and WT. The transformants expressing CDEP1 grew significantly quicker than WT in insects. The transformants expressing CDEP1 were lower in conidial yields on insect cadavers, but insignificantly different from WT.

CONCLUSION

The PEG-mediated protoplast transformation system was effective for L. lecanii, and the expression of CDEP1 significantly enhanced fungal virulence against cotton aphids. © 2016 Society of Chemical Industry.

Pollen size strongly correlates with stigma depth among Pedicularis species

Darwin proposed that pollen size should be positively correlated with stigma depth rather than style length among species given that pollen tubes first enter the stigma autotrophically, then grow through the style heterotrophically. However, studies often show a positive relationship between pollen size and style length. Five floral traits were observed to be correlated among 42 bumblebee-pollinated Pedicularis species (Orobanchaceae) in which stigmas are distinct from styles. The phylogenetic independent contrast analysis revealed that pollen grain volume was more strongly correlated with stigma depth than with style length, consistent with Darwin's functional hypothesis between pollen size and stigma depth.

Genetic improvement of the nematicidal fungus Lecanicillium attenuatum against Heterodera glycines by expression of the Beauveria bassiana Cdep1 protease gene

Lecanicillium attenuatum is an important nematophagous fungus with potential as a biopesticide against plant-parasitic nematodes. The Pr1A-like cuticle-degrading protease (Cdep1) gene originating from the entomopathogenic fungus Beauveria bassiana was transformed into the nematophagous fungus L. attenuatum using a polyethylene-glycol mediated protoplast-based transformation system. Protease activity was increased 0.64- to 1.63-fold 2-10d after growth in the transformed L. attenuatum. Inhibition of egg-hatching and J2 motility of soybean cyst nematodes (Heterodera glycines) by cell-free fungal culture filtrates were enhanced by 17-76% 2-14d and 43-152% 1-13d after incubation, respectively.

[Risk factors of hypoparathyroidism following total or near total thyroidectomy]

OBJECTIVE

To study the risk factors for postoperative hypoparathyroidism or hypocalcemia.

METHODS

Totally 414 patients with thyroid diseases who underwent total or near total thyroidectomy at Department of Head and Neck Surgery, Peking University Cancer Hospital and Institute from June 2007 to June 2014 were studied retrospectively. There were 119 male and 295 female patients with a median age of 47 years. The clinical and pathological features that related to post-operative hypoparathyroidism were studied by χ(2) test and multivariate Logistic regression analysis.

RESULTS

Of the 414 patients, 36.2% developed transient hypocalcemia, 36.5% developed transient hypoparathyroidism, 2.2% developed permanent hypoparathyroidism. In regression analysis, unilateral or bilateral center lymph node dissection were associated with mild transient hypocalcemia after surgery (OR=2.366, P=0.022; OR=5.216, P=0.000); unilateral or bilateral center lymph node dissection as well as surgical options were significant risk factors for severe transient hypocalcemia (OR=4.029, P=0.001; OR=8.384, P=0.000; OR=2.073, P=0.017) and hypoparathyroidism (OR=1.755, P=0.040; OR=4.144, P=0.000; OR=2.287, P=0.000). The parathyroid hormone concentration on postoperative day 1 was an independent risk factor for permanent hypoparathyroidism (OR=2.011, P=0.014). The concentration of parathyroid hormone threshold <5.28 ng/L was a predictor to permanent hypoparathyroidism with accuracy of 95.0%.

CONCLUSIONS

Bilateral center lymph node dissection is a risk factor of permanent hypoparathyroidism in patients received total thyroidectomy should be taken thoughtfully. The parathyroid hormone concentration on postoperative day 1 provides better prediction for persistent hypoparathyroidism.

Protection and Dissection of Recurrent Laryngeal Nerve in Salvage Thyroid Cancer Surgery to Patients with Insufficient Primary Operation Extent and Suspicious Residual Tumor

Some thyroid cancer patients undergone insufficient tumor removal in the primary surgery in China . our aim is to evaluate the impact of dissection of the recurrent laryngeal nerve during a salvage thyroid cancer operation in these patients to prevent nerve injury. Clinical data of 49 enrolled patients who received a salvage thyroid operation were retrospectively reviewed. Primary pathology was thyroid papillary cancer. The initial procedure performed included nodulectomy (20 patients), partial thyroidectomy (19 patients) and subtotal thyroidectomy (10 patients). The effect of dissection and protection of the recurrent laryngeal nerve and the mechanism of nerve injury were studied. The cervical courses of the recurrent laryngeal nerves were successfully dissected in all cases. Nerves were adherent to or involved by scars in 22 cases. Three were ligated near the place where the nerve entered the larynx, while another three were cut near the intersection of inferior thyroid artery with the recurrent laryngeal nerve. Light hoarseness occurred to four patients without a preoperative voice change. In conclusion, accurate primary diagnosis allows for a sufficient primary operation to be performed, avoiding insufficient tumor removal that requires a secondary surgery. The most important cause of nerve damage resulted from not identifying the recurrent laryngeal nerve during first surgery , and meticulous dissection during salvage surgery was the most efficient method to avoid nerve damage.

Distributed parameter model for characterizing magnetic crosstalk in a fiber optic current sensor

The effects of magnetic crosstalk on a fiber optic current sensor are studied using the distributed parameter model. A new method to enhance the immunity to magnetic crosstalk is proposed. The experimental results show that magnetic crosstalk changes periodically with the azimuth angle and decreases as the distance between the conductors increases. When the sensing coil is placed at the optimal azimuth angle, the ratio error from magnetic crosstalk decreases from -0.32% to -0.02%, demonstrating the effectiveness of the proposed method.

Diffusion of a Professional Social Network

Online professional social networks are becoming an instrumental tool to facilitate relationships between business and technology professionals for career success. Even though tools such as LinkedIn can be used to manage human capital for career success use and adoption still is not universally accepted. This paper seeks to better understand the effect university, gender, and degree type has on the diffusion of an online social network (LinkedIn) across three years (2011 to 2014). The authors' findings show diffusion is not consistent across business school graduates. Their business school findings suggest that university, gender, and degree type have significant associations with LinkedIn participation. This is the case even though the majority of graduates still have yet to join the LinkedIn social network. An analysis of the results and future research directions are presented.