The <i>Sinocyclocheilus</i> cavefish genome provides insights into cave adaptation

BACKGROUND: An emerging cavefish model, the cyprinid genus Sinocyclocheilus, is endemic to the massive southwestern karst area adjacent to the Qinghai-Tibetan Plateau of China. In order to understand whether orogeny influenced the evolution of these species, and how genomes change under isolation, especially in subterranean habitats, we performed whole-genome sequencing and comparative analyses of three species in this genus, S. grahami, S. rhinocerous and S. anshuiensis. These species are surface-dwelling, semi-cave-dwelling and cave-restricted, respectively. RESULTS: The assembled genome sizes of S. grahami, S. rhinocerous and S. anshuiensis are 1.75 Gb, 1.73 Gb and 1.68 Gb, respectively. Divergence time and population history analyses of these species reveal that their speciation and population dynamics are correlated with the different stages of uplifting of the Qinghai-Tibetan Plateau. We carried out comparative analyses of these genomes and found that many genetic changes, such as gene loss (e.g. opsin genes), pseudogenes (e.g. crystallin genes), mutations (e.g. melanogenesis-related genes), deletions (e.g. scale-related genes) and down-regulation (e.g. circadian rhythm pathway genes), are possibly associated with the regressive features (such as eye degeneration, albinism, rudimentary scales and lack of circadian rhythms), and that some gene expansion (e.g. taste-related transcription factor gene) may point to the constructive features (such as enhanced taste buds) which evolved in these cave fishes. CONCLUSION: As the first report on cavefish genomes among distinct species in Sinocyclocheilus, our work provides not only insights into genetic mechanisms of cave adaptation, but also represents a fundamental resource for a better understanding of cavefish biology. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12915-015-0223-4) contains supplementary material, which is available to authorized users

Phylogeny of the Labeoninae (Teleostei, Cypriniformes) based on nuclear DNA sequences and implications on character evolution and biogeography

The Labeoninae is a subfamily of the family Cyprinidae, Order Cypriniformes. Oromandibular morphology within the Labeoninae is the greatest among cyprinid fishes. Although several phylogenetic studies about labeonines have been undertaken the results have been inconsistent and a comprehensive phylogeny is needed. Further, an incongruence between morphological and molecular phylogeny requires a systematic exploration of the significance of morphological characters on the basis of the molecular phylogeny. In this study, a total of 292 nucleotide sequences from 73 individuals (representing 24 genera and 73 species) of Labeoninae were analyzed. The results of the phylogenetic analysis indicate that there are four major clades within Labeoninae and three monophyletic lineages within the fourth clade. Results of the character evolution show that all oromandibular morphological characters are homoplastically distributed on the molecular phylogenetic tree and suggests that these chara­cters evolved several times during the history of labeonines. In particular, the labeonine , a specific disc on the lower lip, has been acquired three times and reversed twice. These morphological characters do not have systematic significance but can be useful for taxonomy. The results of biogeography suggest that the Labeoninae originated from Southeast Asia and separately dispersed to Africa, East Asia and South Asia [Current Zoology 58 (6): 837–850, 2012]

Impacts of cropland expansion on carbon storage : A case study in Hubei, China

When cropland expansion encroaches on ecological land (e.g., forest, grassland, wetland), it seriously affects carbon storage which plays an important role in global climate change. Taking Hubei as the study area, this study explored the effects of cropland expansion on carbon storage in both 2000–2010 and 2010–2030 in different scenarios by using the Integrated Valuation of Ecosystem Services and Trade-offs (InVEST) model and the LAND System Cellular Automata model for Potential Effects (LANDSCAPE). The results showed that cropland expansion led to a massive loss of carbon storage (1.76 Tg C) during 2000–2010, which is expected to continue during 2010–2030 in different scenarios. The loss is predicted to be 3.70 Tg C in the Business-As-Usual scenario and be 0.88 Tg C in the Requisition–Compensation Balance of Cropland Policy scenario. Noticeably, the loss of carbon storage due to cropland expansion was 1.12 times more than that due to urban expansion during 2000–2010. For the period of 2010–2030, the loss of carbon storage caused by cropland expansion is predicted to be 3.89 times more than that caused by urban expansion in the Business-As-Usual scenario, while the losses caused by cropland expansion and urban expansion are predicted to be almost equal in the Requisition–Compensation Balance of Cropland Policy scenario. The main cause of carbon storage loss due to cropland expansion is that it leads to the considerable loss of forest and wetland. This study highlights the importance of considering the loss of carbon storage caused by cropland expansion when conducting cropland protection policies and land use planning.</p

Which impacts more seriously on natural habitat loss and degradation? Cropland expansion or urban expansion?

Natural habitat plays an important role in maintaining biodiversity. Both cropland expansion and urban expansion have an influence on natural habitat. However, it is not clear which one impacts more seriously on both the quantity and quality of natural habitat. This study compared the impacts of cropland expansion on the quantity and quality of natural habitat in China between 2000 and 2015 with the impacts of urban expansion. Map algebra in ArcGIS 10.6 was used to calculate the changes in the quantity of natural habitat, while the Integrated Valuation of Ecosystem Services and Trade-offs (InVEST) Habitat Quality model was used to assess the changes in its quality. The results indicated that cropland expansion led to a loss of 35,811 km2 of natural habitat, which was twelve-times as much as that from urban expansion. Furthermore, the area of the heaviest habitat degradation due to cropland expansion was 9,530 km2, which was eight-times as much as that due to urban expansion. Noticeably, the greatest impacts of cropland expansion on natural habitat mostly occurred in areas where the ecological environment is already vulnerable (namely, the resistance and resilience of ecosystems in response to external interference are weak), whereas the impacts of urban expansion were much less in these areas. This study highlights that the impacts of cropland expansion on both the natural habitat loss and degradation far exceeded the impacts of urban expansion. It is necessary to improve cropland protection policies to guarantee food security while ensuring little or no harm to natural habitat

Allelopathic effect of Artemisia argyi on the germination and growth of various weeds

Abstract Allelopathy means that one plant produces chemical substances to affect the growth and development of other plants. Usually, allelochemicals can stimulate or inhibit the germination and growth of plants, which have been considered as potential strategy for drug development of environmentally friendly biological herbicides. Obviously, the discovery of plant materials with extensive sources, low cost and markedly allelopathic effect will have far-reaching ecological impacts as the biological herbicide. At present, a large number of researches have already reported that certain plant-derived allelochemicals can inhibit weed growth. In this study, the allelopathic effect of Artemisia argyi was investigated via a series of laboratory experiments and field trial. Firstly, water-soluble extracts exhibited the strongest allelopathic inhibitory effects on various plants under incubator conditions, after the different extracts authenticated by UPLC-Q-TOF-MS. Then, the allelopathic effect of the A. argyi was systematacially evaluated on the seed germination and growth of Brassica pekinensis, Lactuca sativa, Oryza sativa, Portulaca oleracea, Oxalis corniculata and Setaria viridis in pot experiments, it suggested that the A. argyi could inhibit both dicotyledons and monocotyledons not only by seed germination but also by seedling growth. Furthermore, field trial showed that the A. argyi significantly inhibited the growth of weeds in Chrysanthemum morifolium field with no adverse effect on the growth of C. morifolium. At last, RNA-Seq analysis and key gene detection analysis indicated that A.argyi inhibited the germination and growth of weed via multi-targets and multi-paths while the inhibiting of chlorophyll synthesis of target plants was one of the key mechanisms. In summary, the A. argyi was confirmed as a potential raw material for the development of preventive herbicides against various weeds in this research. Importantly, this discovery maybe provide scientific evidence for the research and development of environmentally friendly herbicides in the future

Hydrochlorothiazide Test as a Tool in the Diagnosis of Gitelman Syndrome in Chinese Patients

Traditional clinical diagnostic criteria for Gitelman syndrome (GS) including hypomagnesemia and hypocalciuria have been challenged by reports of atypical manifestations recently, as well as the development of genetic testing. Hydrochlorothiazide (HCT) test is a diagnostic method different from the traditional biochemical parameters, which could evaluate the function of thiazide-sensitive sodium-chloride co-transporter (NCC) in vivo by a small dose of NCC inhibitor HCT. In this retrospective study, we compared the diagnostic significance of hypomagnesemia, hypocalciuria, and the reaction of HCT test, among Chinese patients with GS confirmed by genetic test. For patients who were clinically suspected of GS manifestations, SLC12A3 gene was sequenced to make genetic diagnosis. A total of 83 GS and 19 control patients were recruited, among which 37 underwent HCT test according to the standard process. Compared with the gold standard of genetic diagnosis, both the diagnostic sensitivity (93.10%) and specificity (100.00%) of the HCT test were much higher than those of hypomagnesemia and/or hypocalciuria. The area under the receiver operating characteristic (ROC) curve was 1.000 (95% CI 0.905–1.000) for HCT test, higher than the values using hypomagnesemia and/or hypocalciuria. The cost of HCT test was around $54, much lower than genetic diagnosis. In conclusion, besides traditional hypomagnesemia and hypocalciuria, HCT test could be a valuable tool in the clinical diagnosis of Chinese GS patients

Mesenchymal stromal cells plus basiliximab improve the response of steroid-refractory acute graft-versus-host disease as a second-line therapy: a multicentre, randomized, controlled trial

Abstract Background For patients with steroid-refractory acute graft-versus-host disease (SR-aGVHD), effective second-line regimens are urgently needed. Mesenchymal stromal cells (MSCs) have been used as salvage regimens for SR-aGVHD in the past. However, clinical trials and an overall understanding of the molecular mechanisms of MSCs combined with basiliximab for SR-aGVHD are limited, especially in haploidentical haemopoietic stem cell transplantation (HID HSCT). Methods The primary endpoint of this multicentre, randomized, controlled trial was the 4-week complete response (CR) rate of SR-aGVHD. A total of 130 patients with SR-aGVHD were assigned in a 1:1 randomization schedule to the MSC group (receiving basiliximab plus MSCs) or control group (receiving basiliximab alone) (NCT04738981). Results Most enrolled patients (96.2%) received HID HSCT. The 4-week CR rate of SR-aGVHD in the MSC group was obviously better than that in the control group (83.1% vs. 55.4%, P = 0.001). However, for the overall response rates at week 4, the two groups were comparable. More patients in the control group used ≥ 6 doses of basiliximab (4.6% vs. 20%, P = 0.008). We collected blood samples from 19 consecutive patients and evaluated MSC-derived immunosuppressive cytokines, including HO1, GAL1, GAL9, TNFIA6, PGE2, PDL1, TGF-β and HGF. Compared to the levels before MSC infusion, the HO1 (P = 0.0072) and TGF-β (P = 0.0243) levels increased significantly 1 day after MSC infusion. At 7 days after MSC infusion, the levels of HO1, GAL1, TNFIA6 and TGF-β tended to increase; however, the differences were not statistically significant. Although the 52-week cumulative incidence of cGVHD in the MSC group was comparable to that in the control group, fewer patients in the MSC group developed cGVHD involving ≥3 organs (14.3% vs. 43.6%, P = 0.006). MSCs were well tolerated, no infusion-related adverse events (AEs) occurred and other AEs were also comparable between the two groups. However, patients with malignant haematological diseases in the MSC group had a higher 52-week disease-free survival rate than those in the control group (84.8% vs. 65.9%, P = 0.031). Conclusions For SR-aGVHD after allo-HSCT, especially HID HSCT, the combination of MSCs and basiliximab as the second-line therapy led to significantly better 4-week CR rates than basiliximab alone. The addition of MSCs not only did not increase toxicity but also provided a survival benefit