Whole‐genome resequencing reveals the pleistocene temporal dynamics of Branchiostoma belcheri and Branchiostoma floridae populations

Global climatic fluctuations governed the ancestral demographic histories of species and contributed to place the current population status into a more extensive ecological and evolutionary context. Genetic variations will leave unambiguous signatures in the patterns of intraspecific genetic variation in extant species since the genome of each individual is an imperfect mosaic of the ancestral genomes. Here, we report the genome sequences of 20 Branchiostoma individuals by whole‐genome resequencing strategy. We detected over 140 million genomic variations for each Branchiostoma individual. In particular, we applied the pairwise sequentially Markovian coalescent (PSMC) method to estimate the trajectories of changes in the effective population size (N_e) of Branchiostoma population during the Pleistocene. We evaluated the threshold of sequencing depth for proper inference of demographic histories using PSMC was ≥25×. The PSMC results highlight the role of historical global climatic fluctuations in the long‐term population dynamics of Branchiostoma. The inferred ancestral N_e of the Branchiostoma belcheri populations from Zhanjiang and Xiamen (China) seawaters was different in amplitude before the first (mutation rate = 3 × 10^?9) or third glaciation (mutation rate = 9 × 10^?9) of the Pleistocene, indicating that the two populations most probably started to evolve in isolation in their respective seas after the first or third glaciation of the Pleistocene. A pronounced population bottleneck coinciding with the last glacial maximum was observed in all Branchiostoma individuals, followed by a population expansion occurred during the late Pleistocene. Species that have experienced long‐term declines may be especially vulnerable to recent anthropogenic activities. Recently, the industrial pollution and the exploitation of sea sand have destroyed the harmonious living environment of amphioxus species. In the future, we need to protect the habitat of Branchiostoma and make full use of these detected genetic variations to facilitate the functional study of Branchiostoma for adaptation to local environments.     

Population genetics and sympatric divergence of the freshwater gudgeon,Gobiobotia filifer,in the Yangtze River inferred from mitochondrial DNA

The ecosystem and Pleistocene glaciations play important roles in population demography. The freshwater gudgeon, Gobiobotia filifer, is an endemic benthic fish in the Yangtze River and is a good model for ecological and evolutionary studies. This study aimed to decode the population structure of G. filifer in the Yangtze River and reveal whether divergence occurred before or after population radiation. A total of 292 specimens from eight locations in the upper and middle reaches of the Yangtze River were collected from 2014 to 2016 and analyzed via mitochondrial DNA Cyt b gene sequencing. A moderately high level of genetic diversity was found without structures among the population. However, phylogenetic and network topology showed two distinct haplotype groups, and each group contained a similar proportion of individuals from all sampled sites. This suggested the existence of two genetically divergent source populations in G. filifer. We deduced that a secondary contact of distinct glacial refugia was the main factor creating sympatric populations of G. filifer, and climate improvement promoted population expansion and colonization.     

Is population subdivision different from speciation? From phylogeography to species delimitation

Species‐level diversity and the underlying mechanisms that lead to the formation of new species, that is, speciation, have often been confounded with intraspecific diversity and population subdivision. The delineation between intraspecific and interspecific divergence processes has received much less attention than species delimitation. The ramifications of confounding speciation and population subdivision are that the term speciation has been used to describe many different biological divergence processes, rendering the results, or inferences, between studies incomparable. Phylogeographic studies have advanced our understanding of how spatial variation in the pattern of biodiversity can begin, become structured, and persist through time. Studies of species delimitation have further provided statistical and model‐based approaches to determine the phylogeographic entities that merit species status. However, without a proper understanding and delineation between the processes that generate and maintain intraspecific and interspecific diversity in a study system, the delimitation of species may still not be biologically and evolutionarily relevant. I argue that variation in the continuity of the divergence process among biological systems could be a key factor leading to the enduring contention in delineating divergence patterns, or species delimitation, meriting future comparative studies to help us better understand the nature of biological species.     

Land masses and oceanic currents drive population structure of Heritiera littoralis,a widespread mangrove in the Indo‐West Pacific

Phylogeographic forces driving evolution of sea‐dispersed plants are often influenced by regional and species characteristics, although not yet deciphered at a large spatial scale for many taxa like the mangrove species Heritiera littoralis. This study aimed to assess geographic distribution of genetic variation of this widespread mangrove in the Indo‐West Pacific region and identify the phylogeographic factors influencing its present‐day distribution. Analysis of five chloroplast DNA fragments’ sequences from 37 populations revealed low genetic diversity at the population level and strong genetic structure of H. littoralis in this region. The estimated divergence times between the major genetic lineages indicated that glacial level changes during the Pleistocene epoch induced strong genetic differentiation across the Indian and Pacific Oceans. In comparison to the strong genetic break imposed by the Sunda Shelf toward splitting the lineages of the Indian and Pacific Oceans, the genetic differentiation between Indo‐Malesia and Australasia was not so prominent. Long‐distance dispersal ability of H. littoralis propagules helped the species to attain transoceanic distribution not only across South East Asia and Australia, but also across the Indian Ocean to East Africa. However, oceanic circulation pattern in the South China Sea was found to act as a barrier creating further intraoceanic genetic differentiation. Overall, phylogeographic analysis in this study revealed that glacial vicariance had profound influence on population differentiation in H. littoralis and caused low genetic diversity except for the refugia populations near the equator which might have persisted through glacial maxima. With increasing loss of suitable habitats due to anthropogenic activities, these findings therefore emphasize the urgent need for conservation actions for all populations throughout the distribution range of H. littoralis.     

国产西罗莫司与原研品在体内外对细胞影响的比较实验

目的探讨国产西罗莫司与原研品对移植宿主外周血中免疫细胞的影响效果。方法体外实验:人膀胱癌T24细胞体外培养,分别加入国产西罗莫司和原研品,CKK-8法检测并比较细胞增殖活性受抑制的情况。体内实验:建立小鼠异位心脏移植模型,设立对照无手术组(对照组)、移植无治疗组(Tx组)、移植+国产西罗莫司组(Tx+YXK组)、移植+原研品组(Tx+RAPA组)。观察移植心脏搏动情况,受者脾脏的流式细胞学检测,以及脾脏及移植物中免疫细胞浸润的病理检查。流式细胞检测树突状细胞(DC),CD8+细胞和调节性T细胞(Treg),病理组织学检测及免疫组化染色比较两组免疫细胞浸润情况。两组间比较采用独立样本t检验,多组间比较采用单因素方差分析,两两比较采用LSD-t检验。结果体外实验结果显示,国产西罗莫司与原研品对T24细胞活力影响的差异无统计学意义(P>0.05)。体内实验结果显示,Tx组移植心脏于第7天停止搏动,Tx+YXK组和Tx+RAPA组在第10天心脏搏动仍有力、节律正常。(1)脾脏流式细胞检测显示,与对照组、Tx组比较,Tx+RAPA组、Tx+YXK组CD11c+I-A+CD86+DC细胞(15.88±4.73、22.90±3.86比4.51±1.57、5.40±2.54)、CD8+淋巴细胞数量(6.32±0.98、6.75±1.34比3.03±1.12、3.23±0.97)均降低,而Tx+RAPA组CD4+CD25+Foxp3+阳性细胞数量(15.06±3.42比7.87±1.95,10.88±2.08)升高(P均<0.05)。Tx+YXK组和Tx+RAPA组3种免疫细胞数量差异均无统计学意义(P>0.05)。(2)移植心脏病理免疫细胞组化染色灰度分析,Tx组、Tx+YXK组和Tx+RAPA组CD4,CD8,IDO和CD11b数量差异无统计学意义(P>0.05),与Tx组比较,Tx+RAPA组和Tx+YXK组CD11c(25143.52±3525.12比12936.30±766.94、14240.60±3124.67)、Foxp3阳性细胞浸润数量(500.78±238.33比46.05±68.16、49.22±25.82)降低(P均<0.05),Tx+YXK组和Tx+RAPA组比较差异无统计学意义(P>0.05)。(3)模型动物脾脏病理免疫细胞组化染色灰度分析,Tx组CD 4和CD8阳性细胞浸润数量较Tx+YXK组和Tx+RAPA组少,但差异无统计学意义(P>0.05),Tx+YXK组和Tx+RAPA组比较,各种细胞染色的IOD值差异均无统计学意义。结论使用国产西罗莫司与原研品两种药物后受者移植心脏和脾脏中的细胞浸润变化一致;在体外对细胞增殖、移植后抗排斥作用和体内免疫细胞的影响表现均一致。     

Dexamethasone does not ameliorate gliosis in a mouse model of neurodegenerative disease

Prolonged neuroinflammation is a driving force for neurodegenerative disease, and agents against inflammatory responses are regarded as potential treatment strategies. Here we aimed to evaluate the prevention effects on gliosis by dexamethasone (DEX), an anti-inflammation drug. We used DEX to treat the nicastrin conditional knockout (cKO) mouse, a neurodegenerative mouse model. DEX (10 mg/kg) was given to 2.5-month-old nicastrin cKO mice, which have not started to display neurodegeneration and gliosis, for 2 months. Immunohistochemistry (IHC) and Western blotting techniques were used to detect changes in neuroinflammatory responses. We found that activation of glial fibrillary acidic protein (GFAP) positive or ionized calcium binding adapter molecule1 (Iba1) positive cells was not inhibited in nicastrin cKO mice treated with DEX as compared to those treated with saline. These data suggest that DEX does not prevent or ameliorate gliosis in a neurodegenerative mouse model when given prior to neuronal or synaptic loss.     

Physiological and molecular advances in magnesium nutrition of plants

Plant and Soil - Phytoremediation of soil contaminated by trace elements is a technology using plants and microorganisms to sequester, inactivate, or extract contaminants from the soil. The...     

Alleviation of Cadmium Toxicity to <i>Medicago Truncatula</i> by AMF Involves the Changes of Cd Speciation in Rhizosphere Soil and Subcellular Distribution

Arbuscular mycorrhizal fungi (AMF) can improve plant tolerance to several abiotic stresses, including heavy metals, drought or salinity exposure. However, the role of AMF in alleviation of soil cadmium (Cd)-induced toxicity to plants is still largely unknown. In this study, Cd speciation in soil and subcellular distribution of Cd were used to characterize the roles of application AM fungi in the alleviation of Cd toxicity in alfalfa plants. Our results showed that the addition of Glomus mosseae in Cd contaminated soil (10 mg/Kg) significantly increased soil pH, cation exchange capacity (CEC) and organic matter in rhizosphere soil with Medicago truncatula L., and then account for significantly decreased contents of exchangeable and carbonate-bounded Cd speciation in rhizosphere soil, indicating alleviation of plant toxicity by reduction of bioavailable fractions of Cd. Although there is no significant difference found in Cd accumulation by roots and shoots respectively between Cd and AM-Cd treatments, more portion of Cd was recorded compartmentalization in cell wall fraction of both root and shoot in treatment of Cd with AM application, indicating alleviation of Cd toxicity to plant cell. Herein, application of AM fungi in Cd treatments performed to inhibit the appearance of Cd toxicity symptoms, including the improvement of leaf electrolyte leakage, root elongation, seedling growth and biomass. This information provides a clearer understanding of detoxification strategy of AM fungi on Cd behavior with development and stabilization of soil structure and subcellular distribution of plant.     

Stool DNA test targeting methylated syndecan-2 (SDC2) as a noninvasive screening method for colorectal cancer

Despite the steadily increasing worldwide incidence of colorectal cancer (CRC), an effective noninvasive approach for early detection of CRC is still under investigation. The guaiac-based fecal occult blood test (FOBT) and fecal immunochemical test (FIT) have gained popularity as noninvasive CRC screening tests owing to their convenience and relatively low costs. However, the FOBT and FIT have limited sensitivity and specificity. To develop a noninvasive tool for the detection of CRC, we investigated the sensitivity, specificity, and accuracy of a stool DNA test targeting methylated syndecan-2 (SDC2), which is frequently methylated in patients with CRC. The present study enrolled 62 patients diagnosed as having stage 0-IV CRC and 76 healthy participants between July 2018 and June 2019 from two institutions. Approximately 4.5 g of stool sample was collected from each participant for detection of human methylated SDC2 gene. In total, 48 of 62 (77.4%) patients with CRC showed positive results, whereas 67 out of 76 (88.2%) healthy participants showed negative results. The area under the curve of the receiver operating characteristic curve constructed was 0.872 for discrimination between patients with CRC and healthy individuals. The present study highlights the potential of the fecal methylated SDC2 test as a noninvasive detection method for CRC screening with a relatively favorable sensitivity of 77.4%, a specificity of 88.2% and a positive predictive value of 84.2% compared with other available fecal tests. Further multicenter clinical trials comprising subjects of varied ethnicities are required to validate this test for the mass screening of patients with CRC.