[Investigation of the immune profile of multiple myeloma patients achieving long-term survival after autologous stem cell transplantation]

Objective: To identify the characteristics of the bone marrow immune microenvironment associated with long-term survival in multiple myeloma (MM) patients. Methods: In the follow-up cohort of patients with newly diagnosed MM and who received "novel agent induction therapy and subsequent autologous stem cell transplantation and immunomodulator maintenance therapy" in the First Affiliated Hospital of Sun Yat-sen University, a cross-sectional study was carried out between August 2019 and May 2020. Using NanoString technology, the RNA expression of 770 bone marrow immune-related markers was compared between 16 patients who had progression-free survival ≥5 years and 5 patients with progressive disease. Among the 16 patients who achieved long-term survival, 9 achieved persistent minimal residual disease (MRD) negative while the other 7 had persistent positive MRD. The functional scores of each kind of immune cells were calculated based on the expression level of characteristic genes, so as to indirectly obtained the proportion of each immune cell subset. The Mann-Whitney U test and the Kruskal Wallis test were used for statistical analysis. Results: The proportion of neutrophils was significantly higher in long-surviving MM patients than in patients with progressive disease [functional scores, 13.61 (13.33, 14.25) vs. 12.93 (12.58, 13.38); Z=2.31, P=0.021]. Among long-surviving patients, those who were MRD-positive had a significantly greater number of mast cells compared with those who were MRD-negative [functional scores, 7.09 (6.49, 8.57) vs. 6.03 (5.18, 6.69); H=2.18, P=0.029]. Compared with patients with progressive disease, four genes (CTSG, IFIT2, S100B, and CHIT1) were significantly downregulated and six (C4B, TNFRSF17, CD70, IRF4, C2, and GAGE1) were upregulated in long-surviving patients. Among long-surviving patients, only gene CMA1 was significantly upgraded, 10 genes (ISG15, OAS3, MX1, IFIT2, DDX58, SIGLEC1, CXCL10, IL1RN, SERPING and TNFSF10) were significantly downregulated in the MRD-positive group compared with that in the MRD-negative group, the first 5 of which are related to the interferon response pathway. Conclusions: The increased neutrophil and mast cell numbers may be related to long-term survival in MM. Interferon signaling activation may be a key bone marrow immune profiling feature for MRD-negative, long-surviving patients with MM.

[The efficacy analysis of neurosurgical robot-assisted DBS in the treatment of elderly Parkinson's disease]

Objective: To investigate the surgical efficacy of neurosurgery robot deep brain stimulation(DBS) in the treatment of elderly Parkinson's disease(PD). Methods: The clinical data of elderly patients (≥75 years) with PD who underwent neurosurgical robot-assisted DBS surgery in the Department of Neurosurgery of the General Hospital of Northern Theater Command from September 2016 to September 2022 were collected retrospectively. Operation time, electrode implantation duration, postoperative pneumocephalus volume, electrode implantation accuracy, the Tao's DBS surgery scale, perioperative complications were analyzed.The unified Parkinson's disease rating scales (UPDRS), UPDRS-Ⅲ, tremor, rigidity, bradykinesia, axial, Barthel Activities of Daily Living (ADL-Barthel), Levodopa Equivalent Daily Dose (LEDD), Montreal Cognitive Assessment (MoCA), Hamilton Anxiety Scale (HAMA) and Hamilton Depression Scale (HAMD) scores and mortality were assessed respectively before operation, 6, 12 and 24 months after operation and last follow-up. Results: A total of 25 elderly patients were enrolled, including 14 males and 11 females, aged(78.3±3.2) years. Nine patients had underlying diseases. Nine patients (36%) underwent bilateral Globus Pallidus pars Interna deep brain stimulation (GPi-DBS) and 16 patients (64%) underwent bilateral subthalamic nucleus deep brain stimulation (STN-DBS).The operation time was (1.56±0.19) hours, the electrode implantation duration was (1.01±0.19) hours, the pneumocephalus volume was 9.8(4.7, 23.3) cm3, and the electrode implantation accuracy was (0.84±0.24) mm, the Tao's DBS surgery scale was (80.2±6.2).The follow-up time [M(Q1, Q3)] was 57.3(27.9, 75.7) months. No serious complications such as intracranial hemorrhage, infection or poor wound healing occurred during the perioperative period. The improvement rate of UPDRS, UPDRS-Ⅲ, rigidity, bradykinesia, and LEDD at 6 months after surgery was significantly higher than that at 24 months after surgery and at the last follow-up (all P<0.05); the improvement rate of axial symptoms, ADL-Barthel score, and MoCA score at 6 months after surgery was significantly higher than that at the last follow-up (P<0.05). HAMD and HAMA scores showed no significant improvement during follow-up after surgery (both P>0.05). At the last follow-up, 12 patients died, with death time of (35.1±20.2) months after operation, and the death age of [M(Q1, Q3)] 80(79, 83)years. Conclusions: Robot-assisted DBS surgery for elderly patients with PD is accurate and safe, and the postoperative symptoms are significantly improved, and they can benefit from neuromodulation for long term, and the risks are controllable.

[New agents-based induction chemotherapy followed by autologous stem cell transplantation and maintenance treatment strategy for multiple myeloma: a single center retrospective study of 300 cases]

Objective: To examine the survival and influential factors of an integrated approach of novel agents, autologous hematopoietic stem cell (auto-HSCT) , and maintenance therapy in patients with multiple myeloma (MM) patients from a single center over the past 15 years. Methods: In our center, 300 MM patients who received an integrated strategy of new agents, auto-HSCT, and maintenance therapy over 15 years were retrospectively and prospectively analyzed. Results: The complete remission rates (CR) and ≥very good partial remission rates (VGPR) following induction therapy, transplantation, and maintenance therapy were respectively 35.3% and 55.2% , 72.4% and 80.0% , 89.2% , and 93.4% . When compared to patients receiving double-drug induction, the ≥VGPR and ORR of patients receiving triple-drug induction were improved. No difference existed in CR, ≥VGPR, and ORR between the PAD (bortezomib + liposome doxorubicin+ dexamethasone) and RAD (lenalidomide + liposome doxorubicin + dexamethasone) regimens, but the benefits speed differed. The negative rate of flow minimal residual disease following induction, transplantation, and maintenance was 18.8% (54 cases) , 41.4% (109 cases) , and 58.7% (142 cases) , respectively. The median time to progress (TTP) was 78.7 months and the median overall survival (OS) was 109 months. The median TTP for RISS-Ⅰ-Ⅲ patients were 111.8 months, 77.4 months, and 30.6 months, and the median OS was 118.8 months, 91.4 months, and 48.5 months, respectively. At various points during treatment, the TTP and OS of patients obtaining CR and MRD negative were longer than those of patients who did not obtain CR and MRD negative. TTP was noticeably shorter in high-risk cytogenetic patients compared to standard-risk patients even when CR was acquired during induction. There was no difference in TTP between patients with high-risk cytogenetics and those with standard-risk cytogenetics if MRD negative was acquired during induction. According to a multivariate analysis, the R-ISS stage was a poor predictor of TTP and OS at various treatment intervals. Therapeutic effectiveness was a newly independent prognostic factor following treatment. Conclusion: A median survival of almost 10 years is possible for MM patients who receive an integrated strategy of induction regimens followed by auto-HSCT and maintenance therapy, which significantly improves prognosis. However, this approach did not significantly benefit high-risk cytogenetic MM patients.

Local adaptation and migratory habits balance spatial-genetic structure between continental and insular chestnut tiger butterflies in East Asia

Geographic and climatic differences between islands and continents may affect the evolution of their biota, and promote divergent selection in species distributed in both landscapes. To assess spatial-genetic structure, we genotyped 18 expressed sequence tag-simple sequence repeat (EST-SSR) loci and sequenced two mtDNA markers (ND5 and COI) and one nuclear marker (EF1α) in two subspecies of the butterfly Parantica sita. Compared with nuclear markers, mtDNA had a stronger signal of population structure. Approximate Bayesian computation (ABC) suggested that a continuous-gene-flow model best described the data. According to this model, the two subspecies diverged approximately 23.1 kya, with ten times more introgression from the continental (ssp. sita) to the insular subspecies (ssp. niphonica) than vice versa. Ecological niche modeling was performed to predict the paleo- and current potential distributions and elucidate the geohistorical process, which revealed a northeastern, insular origin. Winter precipitation and annual temperature range were the main determinants of the subspecies distributions. Maximum-likelihood population-effects models showed that the population differentiation of the insular and continental subspecies was primarily affected by environmental resistance and local climate. Sex-biased migration capacity and long-term precipitation-driven divergence between the continental and insular lineages shaped the current genetic structure of P. sita. Evidence from the nuclear markers confirmed inter-subspecific gene flow despite adaptive divergence between the subspecies. These results imply that the continental subspecies is still capable of returning to the island and introgressing with the insular subspecies.

Cross-sectional associations of device-measured sedentary behaviour and physical activity with cardio-metabolic health in the 1970 British Cohort Study

AIMS

This study aimed to examine the cross-sectional associations of thigh accelerometry-assessed sedentary behaviour and moderate-to-vigorous physical activity (MVPA) with cardio-metabolic health markers and prevalent diabetes in a population sample of middle-aged British adults.

METHODS

Participants (n = 4892) from the age-46-to-48 wave of the 1970 British Cohort Study were fitted with a waterproofed activPAL3 micro device. Total/prolonged sedentary time, breaks and MVPA were the main exposures. We dichotomized prolonged sedentary time and MVPA based on the corresponding median, generating four combinations as categorical exposures. Outcomes comprised of diabetes and seven cardio-metabolic health markers. We used logistic regression and generalized linear models to examine independent/joint associations, conducting a minimally adjusted model including demographics and contextual covariates, and further adjusted for total sedentary time and/or MVPA as applicable.

RESULTS

Each set of 10 sedentary breaks and 1 h of prolonged sedentary time were associated with HbA_1c (mmol/mol) [B = -0.18 (-0.33, -0.03) and 2.35 (1.01, 3.69), respectively]. Each set of 10 sedentary breaks and 1 h of MVPA were favourably associated with diabetes [adjusted odds ratio (AOR): 0.80 (0.71, 0.99) and 0.42 (0.26, 0.67), respectively]. Joint analyses showed that only the low MVPA × long sedentary time combination had significantly higher odds for diabetes than the referent high MVPA × short sedentary time combination [AOR: 1.89 (1.17, 3.03)].

CONCLUSIONS

Each set of additional 10 sedentary breaks per day was associated with 20% lower odds for diabetes. A low physical activity level combined with long sedentary time might synergistically deteriorate cardio-metabolic health.

Niche partitioning among three snail-eating snakes revealed by dentition asymmetry and prey specialisation

The level of dentition asymmetry in snail-eating snakes may reflect their prey choice and feeding efficiency on asymmetric land snails. The three species of Pareas snakes (Squamata: Pareidae) in Taiwan, which form partially sympatric distribution on the island, provide a potential case to test the hypothesis of niche partitioning and character displacement with regard to dentition asymmetry and specialisation in feeding behaviour. In this study, behavioural experiments confirmed that P. formosensis feeds exclusively on slugs, whereas P. atayal and P. komaii consumed both. However, P. atayal more efficiently preys on land snails than P. komaii, exhibiting a shorter handling time and fewer mandibular retractions. Micro-CT and ancestral character reconstruction demonstrated the lowest asymmetry in P. formosensis (the slug specialist), the highest dentition asymmetry in P. atayal (the land snail specialist) and flexibility in P. komaii (the niche switcher): increased dentition asymmetry when sympatrically distributed with the slug eater (character displacement), and decreased asymmetry when living alone (ecological niche release). Ecological niche modelling showed that the distribution of P. formosensis is associated with the presence of slugs, while that of P. atayal could be explained by the land snails. Combining the results from morphology, phylogeny, behavioural experiments and ecological niche modelling, we showed that competition in the sympatric region might have facilitated character displacement among congeners, while the absence of competition in allopatric region has led to ecological niche release.

Historical biogeography of Acer L. (Sapindaceae): genetic evidence for Out-of-Asia hypothesis with multiple dispersals to North America and Europe

Biogeography is the study of where, when, and how modern species evolved and diversified. Acer L. (maple) is one of the most diverse and widespread genera in the Northern Hemisphere. It comprises 124–156 species in the world, approximately 80% species of Acer are native in Asia. The current diversity center of Acer is not congruent with the distribution of the oldest fossils of the genus. Therefore, we herein used 84 species and subspecies to reconstruct the phylogeny and investigate the biogeographic history of Acer using nuclear ITS and three cpDNA fragments (psbA-trnH spacer, rpl16 intron, and trnL-trnF spacer) with maximum likelihood, maximum parsimony, and Bayesian inference methods. The analyses showed that the current diversity center and the origin center of Acer is Asia. Additionally, the North American and Euro-Mediterranean species originated from multiple sources from Asia via the North Atlantic Land Bridge and the Bering Land Bridge, and intercontinental migration has mainly occurred since the Miocene. This study not only provides a novel insight of the origin and dispersal routes of Acer but also exemplifies how past climatic changes affect the diversification-rates of Northern Hemisphere forest trees.

Chloroplast genome of an extremely endangered conifer Thuja sutchuenensis Franch.: gene organization, comparative and phylogenetic analysis

Thuja sutchuenensis is a critically endangered tertiary relict species of Cupressaceae from southwestern China. We sequenced the complete chloroplast (cp) genome of T. sutchuenensis, showing the genome content of 129,776 bp, 118 unique genes including 82 unique protein-coding genes, 32 tRNA genes, and 4 rRNA genes. The genome structures, gene order, and GC content are similar to other typical gymnosperm cp genomes. Thirty-eight simple sequence repeats were identified in the T. sutchuenensis cp genome. We also found an apparent inversion between trnT and psbK between genera Thuja and Thujopsis. In addition, positive selection signals were detected in seven genes with high Ka/Ks ratios. The reconstructed phylogeny based on locally collinear blocks of cp genomes among 21 gymnosperms species is similar to previous inferences. We also inferred a Late-Miocene divergence between T. sutchuenensis and T. standishii, according to the dating of ~ 11.05 Mya by cp genomes. These results will be helpful for future studies of Cupressaceae phylogeny as well as studies in population genetics, systematics, and cp genetic engineering.

Taxonomic notes on Scutellaria taipeiensis (Lamiaceae) from morphological and molecular data

The genus Scutellaria comprises eight species distributed from 50 to 2000 m in Taiwan. Amongst them, S. barbata and S. taipeiensis are very similar on the basis of morphological and plastid DNA sequence information. Therefore, a comprehensive study of the taxonomic status of S. taipeiensis is necessary. We reviewed the herbarium sheets, related literature and protologues and compared morphologies of these two species, as well as their phylogenetic relationships. All evidence, including the diagnostic characters between S. taipeiensis and S. barbata, suggest that they belonged to a single species rather than two. As a result, S. taipeiensis is treated as a synonym of S. barbata.

[High dose melphalan (HDM) is superior to cyclophosphamide plus etoposide and busulfan (CVB) as the conditioning regimen in autologous stem cell transplantation for multiple myeloma]

目的

比较大剂量美法仑（HDM）和环磷酰胺、依托泊苷联合白消安（CVB）预处理方案应用于新诊断多发性骨髓瘤（NDMM）患者自体造血干细胞移植（ASCT）的安全性、近期及远期疗效。

方法

回顾性分析2011年1月至2017年8月期间接受PAD（硼替佐米+脂质体阿霉素+地塞米松）方案诱导治疗序贯ASCT的NDMM患者共123例，按接受预处理方案分为CVB组（82例）和HDM组（41例）。

结果

①非血液学不良反应方面两者无显著区别。②CVB组中性粒细胞植入和血小板植入较HDM组快，中性粒细胞植入时间为第10（9~35）天对第11（9~12）天（z=−3.433，P=0.001）；血小板植入时间为11（7~55）d对HDM组13（10~35）d（z=−3.506，P<0.001）；但CVB组也更早进入粒细胞缺乏（粒缺）及显著血小板减少，最终粒缺及显著血小板减少持续时间两组间尚未显示出差别；但CVB组的发热持续时间以及相应抗生素使用时间显著延长。③CVB组经过移植后获得传统疗效进步的患者比例显著低于HDM组（9/46对14/28，P=0.021）；而且移植后3个月CVB组的微小残留病（MRD）阴性率有低于HDM组的趋势（31.7%对48.8%，P=0.065）。④无论单因素还是多因素分析均显示两种预处理方案并不影响接受PAD诱导序贯ASCT及维持治疗的NDMM患者的至进展时间（TTP）（P= 0.619）及总生存（OS）时间（P=0.295）。

结论

HDM预处理方案血液学不良反应、减低MM肿瘤负荷以及使用方便性方面较CVB方案具有优势，但采用两种预处理方案的ASCT治疗MM的TTP和OS未见明显差异。

[Bortezomib-based induction chemotherapy followed by autologous hematopoietic stem cell transplantation and maintenance in 200 patients with multiple myeloma: long-term follow-up results from single center]

Objective: To study the efficacy, safety and long-term outcomes of integrated strategy of bortezomib-based induction regimens followed by autologous hematopoietic stem cell (ASCT) and maintenance therapy in Chinese multiple myeloma (MM) patients. Methods: 200 MM patients receiving integrated strategy of bortezomib--based induction regimens followed by ASCT and maintenance therapy were retrospectively and prospectively analyzed from December 1. 2006 to April 30. 2018. Results: The complete remission rates (CR) and better than very good partial remission rates (VGPR) after induction therapy, transplantation and maintenance therapy were respectively 31% and 75.5%, 51.8% and 87.7%,73.6% and 93.4%. There was no difference between 4 cycles and more than 5 cycles induction chemotherapy. The negative rate of MRD detection by flow cytometry was 17.6% and 38.2% respectively after induction and 3 months after transplantation. The negative rate of MRD gradually increased during the maintenance therapy. The success rate of high dose CTX combined with G-CSF mobilization was 95.5% and transplantation related mortality (TRM) was zero. The median time to progress (TTP) was 75.3 months and the median overall survival (OS) was 99.5 months. TTP of patients obtaining CR and negative MRD after induction were longer that those of no CR and positive MRD. TTP and OS of patients receiving triple-drug induction and ASCT in early stage were longer than those of double-drug induction and ASCT in late stage. LDH≥240 U/L, high risk cytogenetics, ISS II+III stage and HBsAg positive were prognostic factors at diagnosis. However, only MRD and high risk cytogenetics were independent prognostic factors after transplantation and maintenance therapy. The clinical characteristics of patients of TTP ≥6 years were listed below: light-chain type M protein, ISS I stage, normal level of hemoglobin and platelet, normal LDH, HBsAg negative, chromosome 17p-negative, good response and sustained good response. Conclusions: Integrated strategy of bortezomib-based induction regimens followed by ASCT and maintenance therapy can significantly improve the short-term and long-term efficacy. The prognostic factors of TTP in different disease stages were different. Response to treatment, especially MRD, played a more important role in prognostic factors.

The effects of afforestation on soil bacterial communities in temperate grassland are modulated by soil chemical properties

Grassland afforestation dramatically affects the abiotic, biotic, and ecological function properties of the original ecosystems. Interference from afforestation might disrupt the stasis of soil physicochemical properties and the dynamic balance of microbiota. Some studies have suggested low sensitivity of soil properties and bacterial community to afforestation, but the apparent lack of a significant relationship is probably due to the confounding effects of the generalist habitat and rare bacterial communities. In this study, soil chemical and prokaryotic properties in a 30-year-old Mongolia pine (Pinus sylvestris var. mongolica Litv.) afforested region and adjacent grassland in Inner Mongolia were classified and quantified. Our results indicate that the high richness of rare microbes accounts for the alpha-diversity of the soil microbiome. Few OTUs of generalist (core bacteria) and habitat-specialist bacteria are present. However, the high abundance of this small number of OTUs governs the beta-diversity of the grassland and afforested land bacterial communities. Afforestation has changed the soil chemical properties, thus indirectly affecting the soil bacterial composition rather than richness. The contents of soil P, Ca²⁺, and Fe³⁺ account for differentially abundant OTUs such as Planctomycetes and subsequent changes in the ecologically functional potential of soil bacterial communities due to grassland afforestation. We conclude that grassland afforestation has changed the chemical properties and composition of the soil and ecological functions of the soil bacterial community and that these effects of afforestation on the microbiome have been modulated by changes in soil chemical properties.

Nuclear and chloroplast DNA phylogeography suggests an Early Miocene southward expansion of Lithocarpus (Fagaceae) on the Asian continent and islands

BACKGROUND

Most genera of Fagaceae are thought to have originated in the temperate regions except for the genus Lithocarpus, the stone oaks. Lithocarpus is distributed in subtropical and tropical Asia, and its ancestral population is hypothesized to be distributed in tropical regions in Borneo and Indochina. Borneo and the nearby islands (the Greater Sunda Islands) were connected to the Malay Peninsula and Indochina prior to the Pliocene epoch and formed the former Sundaland continent. The Southeast Asian Lithocarpus, is thought to have dispersed between continental Asia and the present Sundaland. The drastic climate changes during the Pliocene and Pleistocene epochs which caused periodic sea-level changes is often used to explain the cause of its diversity. The aim of this study was to establish phylogenetic relationships by analyzing nuclear (nrDNA) and chloroplast (cpDNA) DNA in order to describe and analyze the origin, causes of diversification and historical biogeography of Lithocarpus.

RESULTS

Phylogeny reconstructed through the multiple-species coalescent method with nrDNA and cpDNA revealed that the continental-Asian taxa were clustered at the basal lineages. The derived lineages of tropical Lithocarpus, with the inference of a subtropical ancestral state, imply a southward migration in the Early Miocene period with subsequent in situ diversification in the Greater Sunda Islands. The gradual decrease in temperature since the Middle Miocene period is proposed as a cause of the increase in the net diversification rate.

CONCLUSIONS

The historical ancestral origin of Lithocarpus has been suggested to be mainland Asia. Southward migration in the Early Miocene period with subsequent in situ diversification could explain the current diversity of stone oaks in Southeast Asia. This study also considered the multiple origins of stone oaks currently indigenous to the subtropical islands offshore and near mainland China. Our results provide phylogenetic evidence for a subtropical origin of Asian stone oaks and reveal the process of diversification and how it fits into the timeline of major geologic and climatic events rather than local, episodic, rate-shifting events.

Differential genetic responses to the stress revealed the mutation-order adaptive divergence between two sympatric ginger species

BACKGROUND

Divergent genetic responses to the same environmental pressures may lead sympatric ecological speciation possible. Such speciation process possibly explains rapid sympatric speciation of island species. Two island endemic ginger species Zingiber kawagoii and Z. shuanglongensis was suggested to be independently originated from inland ancestors, but their island endemism and similar morphologies and habitats lead another hypothesis of in situ ecological speciation. For understanding when and how these two species diverged, intraspecific variation was estimated from three chloroplast DNA fragments (cpDNA) and interspecific genome-wide SNPs and expression differences after saline treatment were examined by transcriptomic analyses.

RESULTS

Extremely low intraspecific genetic variation was estimated by cpDNA sequences in both species: nucleotide diversity π = 0.00002 in Z. kawagoii and no nucleotide substitution but only indels found in Z. shuanglongensis. Nonsignificant inter-population genetic differentiation suggests homogenized genetic variation within species. Based on 53,683 SNPs from 13,842 polymorphic transcripts, in which 10,693 SNPs are fixed between species, Z. kawagoii and Z. shuanglongensis were estimated to be diverged since 218~ 238 thousand generations ago (complete divergence since 41.5~ 43.5 thousand generations ago). This time is more recent than the time of Taiwan Island formation. In addition, high proportion of differential expression genes (DEGs) is non-polymorphic or non-positively selected, suggesting key roles of plastic genetic divergence in broaden the selectability in incipient speciation. While some positive selected DEGs were mainly the biotic and abiotic stress-resistance genes, emphasizing the importance of adaptive divergence of stress-related genes in sympatric ecological speciation. Furthermore, the higher proportional expression of functional classes in Z. kawagoii than in Z. shuanglongensis explains the more widespread distribution of Z. kawagoii in Taiwan.

CONCLUSIONS

Our results contradict the previous hypothesis of independent origination of these two island endemic ginger species from SE China and SW China. Adaptive divergent responses to the stress explain how these gingers maintain genetic differentiation in sympatry. However, the recent speciation and rapid expansion make extremely low intraspecific genetic variation in these two species. This study arise a more probable speciation hypothesis of sympatric speciation within an island via the mutation-order mechanism underlying the same environmental pressure.

Molecular genetic and biochemical evidence for adaptive evolution of leaf abaxial epicuticular wax crystals in the genus Lithocarpus (Fagaceae)

BACKGROUND

Leaf epicuticular wax is an important functional trait for physiological regulation and pathogen defense. This study tests how selective pressure may have forced the trait of leaf abaxial epicuticular wax crystals (LAEWC) and whether the presence/absence of LAEWC is associated with other ecophysiological traits. Scanning Electron Microscopy was conducted to check for LAEWC in different Lithocarpus species. Four wax biosynthesis related genes, including two wax backbone genes ECERIFERUM 1 (CER1) and CER3, one regulatory gene CER7 and one transport gene CER5, were cloned and sequenced. Ecophysiological measurements of secondary metabolites, photosynthesis, water usage efficiency, and nutrition indices were also determined. Evolutionary hypotheses of leaf wax character transition associated with the evolution of those ecophysiological traits as well as species evolution were tested by maximum likelihood.

RESULTS

Eight of 14 studied Lithocarpus species have obvious LAEWC appearing with various types of trichomes. Measurements of ecophysiological traits show no direct correlations with the presence/absence of LAEWC. However, the content of phenolic acids is significantly associated with the gene evolution of the wax biosynthetic backbone gene CER1, which was detected to be positively selected when LAEWC was gained during the late-Miocene-to-Pliocene period.

CONCLUSIONS

Changes of landmass and vegetation type accelerated the diversification of tropical and subtropical forest trees and certain herbivores during the late Miocene. As phenolic acids were long thought to be associated with defense against herbivories, co-occurrence of LAEWC and phenolic acids may suggest that LAEWC might be an adaptive defensive mechanism in Lithocarpus.

The Aboveground Vegetation Type and Underground Soil Property Mediate the Divergence of Soil Microbiomes and the Biological Interactions

The composition of the soil microbiome is influenced by environmental (abiotic) variables and biological interactions (biotic factors). To determine whether the aboveground vegetation and soil physicochemical properties were the main determinant of beta-diversity and biological interaction of soil microbial community, we sampled soils from the temperate coniferous forest and grassland. Clustering of operational taxonomic units was conducted using 16S rRNA gene. We found that the microbial composition of the rhizospheres, in which root exudates influence the microbial environment, show lower alpha-diversity than that of nonroot soils. The nonsignificant rhizosphere effect suggested other undetermined factors or stochastic processes accounted for microbial diversity in the rhizosphere. More significant microbe-microbe interactions were observed in forest and rhizosphere soils relative to the grassland soils. The elevated number of positive correlations for relative abundances in forest soil implied beneficial associations being common among bacteria, in particular within the rhizosphere environment. The particular soil properties generated by root exudates also alter the physicochemical properties of soil such as K and pH value, and might in turn favor the adoption of teamwork-cooperation strategies for microbe-microbe interactions, represented as large clusters of positive associations among bacterial taxa. Specific biological interactions differentiated the microbiomes within forest soils. Thus, the environmental selection pressure of aboveground vegetation accounts for differences between soil microbiomes while biotic factors are responsible for fine-scale differences of the microbial community in forest soils.

Composition and Functional Specialists of the Gut Microbiota of Frogs Reflect Habitat Differences and Agricultural Activity

The physiological impact of agricultural pollution, habitat disturbance, and food source variability on amphibian remains poorly understood. By comparing the composition and predicted functions of gut microbiota of two frog species from forest and farmland, we quantified the effects of the exogenous environment and endogenous filters on gut microbiota and the corresponding functions. However, compositional differences of the gut microbiota between the frog species were not detected, even when removing roughly 80–88% of the confounding effect produced by common and shared bacteria (i.e., generalists) and those taxa deemed too rare. The habitat effect accounted for 14.1% of the compositional difference of gut microbial specialists, but host and host × habitat effects were not significant. Similar trends of a significant habitat effect, at an even higher level (26.0%), for the physiological and metabolic functions of gut microbiota was predicted. A very obvious skewing of the relative abundance of functional groups toward farmland habitats reflects the highly diverse bacterial functions of farmland frogs, in particular related to pathogenic disease and pesticide degradation, which may be indication of poor adaptation or strong selective pressure against disease. These patterns reflect the impacts of agricultural activities on frogs and how such stresses may be applied in an unequal manner for different frog species.

Functional divergence and intron variability during evolution of angiosperm TERMINAL FLOWER1 (TFL1) genes

The protein encoded by the TERMINAL FLOWER1 (TFL1) gene maintains indeterminacy in inflorescence meristem to repress flowering, and has undergone multiple duplications. However, basal angiosperms have one copy of a TFL1-like gene, which clusters with eudicot TFL1/CEN paralogs. Functional conservation has been reported in the paralogs CENTRORADIALIS (CEN) in eudicots, and ROOTS CURL IN NPA (RCNs) genes in monocots. In this study, long-term functional conservation and selective constraints were found between angiosperms, while the relaxation of selective constraints led to subfunctionalisation between paralogs. Long intron lengths of magnoliid TFL1-like gene contain more conserved motifs that potentially regulate TFL1/CEN/RCNs expression. These might be relevant to the functional flexibility of the non-duplicate TFL1-like gene in the basal angiosperms in comparison with the short, lower frequency intron lengths in eudicot and monocot TFL1/CEN/RCNs paralogs. The functionally conserved duplicates of eudicots and monocots evolved according to the duplication-degeneration-complementation model, avoiding redundancy by relaxation of selective constraints on exon 1 and exon 4. These data suggest that strong purifying selection has maintained the relevant functions of TFL1/CEN/RCNs paralogs on flowering regulation throughout the evolution of angiosperms, and the shorter introns with radical amino acid changes are important for the retention of paralogous duplicates.

Continuation of the genetic divergence of ecological speciation by spatial environmental heterogeneity in island endemic plants

Divergent selection plays a critical role not only as a speciation driver but also in maintaining post-speciation divergence. In the absence of direct evidence, ancestral interspecific gene flow between incipient species can reflect ancient selective pressure for ecological speciation. In the present study, two late-Pleistocene diverged species endemic to Taiwan, Scutellaria playfairii and S. tashiroi, were spatially and ecologically partitioned with partial overlap. Multilocus genome-scan analyses and in silico evaluation revealed ancestral interspecific gene flow but distinct genetic compositions, implying that adaptive divergence contributed to their speciation. Ecological niche modeling and principal component analysis suggested incomplete divergent niches between the two species; the species distribution is therefore consistent with Hutchinson's metaphor of multidimensional hypervolume niches rather than attributable to a single factor. Constraint ordination analysis supported this inference of a combination of variables explaining the genetic structure. The rare occurrence of hybrids in the sympatric population suggested hybrid breakdown, providing further evidence of divergent selection blocking gene flow. The correlation of environmental variables with integrated genetic components demonstrated that environmental heterogeneity maintains the species and population differentiation. This study highlights the importance of environmental heterogeneity and divergent selection for the rapid speciation and recent diversification of island plants.

Local Climate Heterogeneity Shapes Population Genetic Structure of Two Undifferentiated Insular Scutellaria Species

Spatial climate heterogeneity may not only affect adaptive gene frequencies but could also indirectly shape the genetic structure of neutral loci by impacting demographic dynamics. In this study, the effect of local climate on population genetic variation was tested in two phylogenetically close Scutellaria species in Taiwan. Scutellaria taipeiensis, which was originally assumed to be an endemic species of Taiwan Island, is shown to be part of the widespread species S. barbata based on the overlapping ranges of genetic variation and climatic niches as well as their morphological similarity. Rejection of the scenario of "early divergence with secondary contact" and the support for multiple origins of populations of S. taipeiensis from S. barbata provide strong evolutionary evidence for a taxonomic revision of the species combination. Further tests of a climatic effect on genetic variation were conducted. Regression analyses show nonlinear correlations among any pair of geographic, climatic, and genetic distances. However, significantly, the bioclimatic variables that represent the precipitation from late summer to early autumn explain roughly 13% of the genetic variation of our sampled populations. These results indicate that spatial differences of precipitation in the typhoon season may influence the regeneration rate and colonization rate of local populations. The periodic typhoon episodes explain the significant but nonlinear influence of climatic variables on population genetic differentiation. Although, the climatic difference does not lead to species divergence, the local climate variability indeed impacts the spatial genetic distribution at the population level.

Imbalanced positive selection maintains the functional divergence of duplicated DIHYDROKAEMPFEROL 4-REDUCTASE genes

Gene duplication could be beneficial by functional division but might increase the risk of genetic load. The dynamics of duplicated paralogs number could involve recombination, positive selection, and functional divergence. Duplication of DIHYDROFLAVONOL 4-REDUCTASE (DFR) has been reported in several organisms and may have been retained by escape from adaptive conflict (EAC). In this study, we screened the angiosperm DFR gene focusing on a diversified genus Scutellaria to investigate how these duplicated genes are retained. We deduced that gene duplication involved multiple independent events in angiosperms, but the duplication of DFR was before the divergence of Scutellaria. Asymmetric positive selective pressures resulted in different evolutionary rates between the duplicates. Different numbers of regulatory elements, differential codon usages, radical amino acid changes, and differential gene expressions provide evidences of functional divergence between the two DFR duplicates in Scutellaria, implying adaptive subfunctionalization between duplicates. The discovery of pseudogenes accompanying a reduced replacement rate in one DFR paralogous gene suggested possibly leading to “loss of function” due to dosage imbalance after the transient adaptive subfunctionalization in the early stage of duplication. Notwithstanding, episodic gene duplication and functional divergence may be relevant to the diversification of ecological function of DFR gene in Scutellaria.

Diversifying selection of the anthocyanin biosynthetic downstream gene UFGT accelerates floral diversity of island Scutellaria species

BACKGROUND

Adaptive divergence, which usually explains rapid diversification within island species, might involve the positive selection of genes. Anthocyanin biosynthetic pathway (ABP) genes are important for floral diversity, and are related to stress resistance and pollination, which could be responsible for species diversification. Previous studies have shown that upstream genes of ABP are subject to selective constraints and have a slow evolutionary rate, while the constraints on downstream genes are lower.

RESULTS

In this study, we confirmed these earlier observations of heterogeneous evolutionary rate in upstream gene CHS and the downstream gene UFGT, both of which were expressed in Scutellaria sp. inflorescence buds. We found a higher evolutionary rate and positive selection for UFGT. The codons under positive selection corresponded to the diversified regions, and the presence or absence of an α-helix might produce conformation changes in the Rossmann-like fold structure. The significantly high evolutionary rates for UFGT genes in Taiwanese lineages suggested rapid accumulation of amino acid mutations in island species. The results showed positive selection in closely related species and explained the high diversification of floral patterns in these recently diverged species. In contrast, non-synonymous mutation rate decreases in long-term divergent species could reduce mutational load and prevent the accumulation of deleterious mutations.

CONCLUSIONS

Together with the positive selection of transcription factors for ABP genes described in a previous study, these results confirmed that positive selection takes place at a translational level and suggested that the high divergence of ABP genes is related to the floral diversity in island Scutellaria species.

Changes of diet and dominant intestinal microbes in farmland frogs

BACKGROUND

Agricultural activities inevitably result in anthropogenic interference with natural habitats. The diet and the gut microbiota of farmland wildlife can be altered due to the changes in food webs within agricultural ecosystems. In this work, we compared the diet and intestinal microbiota of the frog Fejervarya limnocharis in natural and farmland habitats in order to understand how custom farming affects the health of in vivo microbial ecosystems.

RESULTS

The occurrence, abundance, and the numbers of prey categories of stomach content were significantly different between the frogs inhabiting natural and farmland habitats. In addition, differences in the abundance, species richness, and alpha-diversity of intestinal microbial communities were also statistically significant. The microbial composition, and particularly the composition of dominant microbes living in intestines, indicated that the land use practices might be one of factors affecting the gut microbial community composition. Although the first three dominant microbial phyla Bacteroidetes, Firmicutes, and Proteobacteria found in the intestines of frogs were classified as generalists among habitats, the most dominant gut bacterial phylum Bacteroidetes in natural environments was replaced by the microbial phylum Firmicutes in farmland frogs. Increased intestinal microbial richness of the farmland frogs, which is mostly contributed by numerous microbial species of Proteobacteria, Actinobacteria, Acidobacteria, and Planctomycetes, not only reflects the possible shifts in microbial community composition through the alteration of external ecosystem, but also indicates the higher risk of invasion by disease-related microbes.

CONCLUSIONS

This study indicates that anthropogenic activities, such as the custom farming, have not only affected the food resources of frogs, but also influenced the health and in vivo microbial ecosystem of wildlife.

Recurrent positive selection and heterogeneous codon usage bias events leading to coexistence of divergent pigeon circoviruses

The capsid genes from 14 pigeon circovirus (PiCV) sequences, collected from Taiwan between 2009 and 2010, were sequenced and compared with 14 PiCV capsid gene sequences from GenBank. Based on pairwise comparison, PiCV strains from Taiwan shared 73.9-100% nucleotide identity and 72-100% amino acid identity with those of the 14 reported PiCV sequences. Phylogenetic analyses revealed that Taiwanese PiCV isolates can be grouped into two clades: clade 1 comprising isolates from Belgium, Australia, USA, Italy and China, and clade 2 showing close relation to isolates from Germany and France. Recurrent positive selection was detected in clade 1 PiCV lineages, which may contribute to the diversification of predominant PiCV sequences in Taiwan. Further observations suggest that synonymous codon usage variations between PiCV clade 1 and clade 2 may reflect the adaptive divergence on translation efficiency of capsid genes in infectious hosts. Variation in selective pressures acting on the evolutionary divergence and codon usage bias of both clades explains the regional coexistence of virus sequences congeners prevented from competitive exclusion within an island such as Taiwan. Our genotyping results also provide insight into the aetiological agents of PiCV outbreak in Taiwan and we present a comparative analysis of the central coding region of PiCV genome. From the sequence comparison results of 28 PiCVs which differs in regard to the geographical origin and columbid species, we identified conserved regions within the capsid gene that are likely to be suitable for primer selection and vaccine development.

Positive selection and functional divergence of R2R3-MYB paralogous genes expressed in inflorescence buds of Scutellaria species (Labiatae)

Anthocyanin is the main pigment forming floral diversity. Several transcription factors that regulate the expression of anthocyanin biosynthetic genes belong to the R2R3-MYB family. Here we examined the transcriptomes of inflorescence buds of Scutellaria species (skullcaps), identified the expression R2R3-MYBs, and detected the genetic signatures of positive selection for adaptive divergence across the rapidly evolving skullcaps. In the inflorescence buds, seven R2R3-MYBs were identified. MYB11 and MYB16 were detected to be positively selected. The signature of positive selection on MYB genes indicated that species diversification could be affected by transcriptional regulation, rather than at the translational level. When comparing among the background lineages of Arabidopsis, tomato, rice, and Amborella, heterogeneous evolutionary rates were detected among MYB paralogs, especially between MYB13 and MYB19. Significantly different evolutionary rates were also evidenced by type-I functional divergence between MYB13 and MYB19, and the accelerated evolutionary rates in MYB19, implied the acquisition of novel functions. Another paralogous pair, MYB2/7 and MYB11, revealed significant radical amino acid changes, indicating divergence in the regulation of different anthocyanin-biosynthetic enzymes. Our findings not only showed that Scutellaria R2R3-MYBs are functionally divergent and positively selected, but also indicated the adaptive relevance of regulatory genes in floral diversification.

Tracing evolutionary relicts of positive selection on eight malaria-related immune genes in mammals

Plasmodium-induced malaria widely infects primates and other mammals. Multiple past studies have revealed that positive selection could be the main evolutionary force triggering the genetic diversity of anti-malaria resistance-associated genes in human or primates. However, researchers focused most of their attention on the infra-generic and intra-specific genome evolution rather than analyzing the complete evolutionary history of mammals. Here we extend previous research by testing the evolutionary link of natural selection on eight candidate genes associated with malaria resistance in mammals. Three of the eight genes were detected to be affected by recombination, including TNF-α, iNOS and DARC. Positive selection was detected in the rest five immunogenes multiple times in different ancestral lineages of extant species throughout the mammalian evolution. Signals of positive selection were exposed in four malaria-related immunogenes in primates: CCL2, IL-10, HO1 and CD36. However, selection signals of G6PD have only been detected in non-primate eutherians. Significantly higher evolutionary rates and more radical amino acid replacement were also detected in primate CD36, suggesting its functional divergence from other eutherians. Prevalent positive selection throughout the evolutionary trajectory of mammalian malaria-related genes supports the arms race evolutionary hypothesis of host genetic response of mammalian immunogenes to infectious pathogens.

Asymmetric introgression in the horticultural living fossil cycas sect. Asiorientales using a genome-wide scanning approach

The Asian cycads are mostly allopatric, distributed in small population sizes. Hybridization between allopatric species provides clues in determining the mechanism of species divergence. Horticultural introduction provides the chance of interspecific gene flow between allopatric species. Two allopatrically eastern Asian Cycas sect. Asiorientales species, C. revoluta and C. taitungensis, which are widely distributed in Ryukyus and Fujian Province and endemic to Taiwan, respectively, were planted in eastern Taiwan for horticultural reason. Higher degrees of genetic admixture in cultivated samples than wild populations in both cycad species were detected based on multilocus scans by neutral AFLP markers. Furthermore, bidirectional but asymmetric introgression by horticultural introduction of C. revoluta is evidenced by the reanalyses of species associated loci, which are assumed to be diverged after species divergence. Partial loci introgressed from native cycad to the invaders were also detected at the loci of strong species association. Consistent results tested by all neutral loci, and the species-associated loci, specify the recent introgression from the paradox of sharing of ancestral polymorphisms. Phenomenon of introgression of cultivated cycads implies niche conservation among two geographic-isolated cycads, even though the habitats of the extant wild populations of two species are distinct.

Diversification, biogeographic pattern, and demographic history of Taiwanese Scutellaria species inferred from nuclear and chloroplast DNA

The ragged topography created by orogenesis generates diversified habitats for plants in Taiwan. In addition to colonization from nearby mainland China, high species diversity and endemism of plants is also present in Taiwan. Five of the seven Scutellaria species (Lamiaceae) in Taiwan, for example, are endemic to the island. Hypotheses of multiple sources or in situ radiation have arisen to explain the high endemism of Taiwanese species. In this study, phylogenetic analyses using both nuclear and chloroplast markers revealed the multiple sources of Taiwanese Scutellaria species and confirmed the rapid and recent speciation of endemic species, especially those of the "indica group" composed of S. indica, S. austrotaiwanensis, S. tashiroi, and S. playfairii. The common ancestors of the indica group colonized first in northern Taiwan and dispersed regionally southward and eastward. Climate changes during glacial/interglacial cycles led to gradual colonization and variance events in the ancestors of these species, resulting in the present distribution and genetic differentiation of extant populations. Population decline was also detected in S. indica, which might reflect a bottleneck effect from the glacials. In contrast, the recently speciated endemic members of the indica group have not had enough time to accumulate much genetic variation and are thus genetically insensitive to demographic fluctuations, but the extant lineages were spatially expanded in the coalescent process. This study integrated phylogenetic and population genetic analyses to illustrate the evolutionary history of Taiwanese Scutellaria of high endemism and may be indicative of the diversification mechanism of plants on continental islands.

Characterization of 24 transferable microsatellite loci in four skullcaps (Scutellaria, Labiatae)

PREMISE OF THE STUDY

Transferable polymorphic microsatellite loci for four skullcaps, Scutellaria indica, S. taiwanensis, S. austrotaiwanensis, and S. playfairii, were developed for future studies of the mating system and population structure of these species. Interspecific amplification was also tested in various Scutellaria species.

METHODS AND RESULTS

Twelve novel polymorphic microsatellite loci were isolated from four S. taiwanensis specimens, and seven are interspecifically transferable. Microsatellite loci developed from S. austrotaiwanensis in a previous study were also analyzed in the other three species, and 12 loci were found to be transferable. Allele numbers of the total 24 loci for S. indica, S. taiwanensis, S. playfairii, and S. austrotaiwanensis are two to four, two, two to five, and two to three, respectively, with an expected heterozygosity ranging from 0.114-0.661, 0.062-0.499, 0.280-0.730, and 0.268-0.662, respectively. The interspecies transferability of these 24 loci was further tested in another 10 Scutellaria species, including three species native to Taiwan. Seventeen loci were found to be interspecifically amplifiable, especially among the Taiwan native species.

CONCLUSIONS

These highly polymorphic and transferable loci will be useful for future studies of the mating system of closely related Scutellaria species.

Microbial community composition of the Danshui river estuary of Northern Taiwan and the practicality of the phylogenetic method in microbial barcoding

In this study, the microbial community in a mangrove ecosystem was surveyed and used to test the eligibility of 16S rDNA library and neighbor-joining method for the purpose of estimating microbial composition. Genetic diversity (pi) and four other diversity indices (Simpson's unbiased, Shannon-Wiener, Evenness, and Chao1 indices) were applied to estimate the adaptive lineages of microorganisms in the mangrove ecosystem. The results indicated that gamma-Proteobacteria is the most diverse taxon, while the most abundant family is Rhodobacteraceae (alpha-Proteobacteria), followed by Comamonadaceae (beta-Proteobacteria). This result may imply the existence of a graded distribution of microbial diversity across a spectrum of different salinities in the waterbody of this estuary ecosystem. Furthermore, at least 500-1,000 bps of the posterior portion of 16S rDNA is required as a marker to profile the microbial diversity in a microcosm of interest using phylogenetic methods, according to the results of our sliding window analyses for the measurements of pi, consistency index, and retention index.

Inhibition of histone deacetylase 2 increases apoptosis and p21Cip1/WAF1 expression, independent of histone deacetylase 1

Histone deacetylases (HDACs) 1 and 2 share a high degree of homology and coexist within the same protein complexes. Despite their close association, each possesses unique functions. We show that the upregulation of HDAC2 in colorectal cancer occurred early at the polyp stage, was more robust and occurred more frequently than HDAC1. Similarly, while the expression of HDACs1 and 2 were increased in cervical dysplasia and invasive carcinoma, HDAC2 expression showed a clear demarcation of high-intensity staining at the transition region of dysplasia compared to HDAC1. Upon HDAC2 knockdown, cells displayed an increased number of cellular extensions reminiscent of cell differentiation. There was also an increase in apoptosis, associated with increased p21Cip1/WAF1 expression that was independent of p53. These results suggest that HDACs, especially HDAC2, are important enzymes involved in the early events of carcinogenesis, making them candidate markers for tumor progression and targets for cancer therapy.

American ginseng extract reduces scopolamine-induced amnesia in a spatial learning task

OBJECTIVE

To determine if HT-1001, an extract of American ginseng, affects scopolamine-induced memory and performance deficits in a spatial learning task, alters brain concentrations of aminergic neurotransmitters, and alters choline uptake in synaptosome preparations.

DESIGN

Animal study.

ANIMALS

48 Sprague Dawley rats.

INTERVENTIONS

Long-term oral administration of a test material or control solution. Intraperitoneal administration of scopolamine (2 mg/kg) 30 minutes before testing.

OUTCOME MEASURES

Performance on Morris water maze task, choline uptake, aminergic neurotransmitter analysis, in vitro monoamine oxidase analysis (of compounds).

RESULTS

HT-1001 protected against scopolamine-induced amnesia and increased choline uptake in synaptosomal preparations. HT-1001 did not alter brain concentrations of norepinephrine, dopamine, 5-HT (serotonin), 3,4-dihydroxyphenylacetic acid or 5-hydroxyindoleactic acid. HT-1001 had a very weak ability to inhibit monoamine oxidase activity in vitro.

CONCLUSIONS

HT-1001 demonstrates a capacity to protect against scopolamine-induced memory deficits.