[Efficacy and safety of first-line treatment with anti-CD38 monoclonal antibody-based regimen for primary plasma cell leukemia]

Objective: To analyze the efficacy and safety of first-line treatment with an anti-CD38 monoclonal antibody regimen for primary plasma cell leukemia (pPCL). Methods: Patients diagnosed with pPCL from December 1st, 2018 to July 26th, 2023, receiving first-line treatment of anti-CD38 monoclonal antibody-based regimens across multiple centers including Peking University People's Hospital, Fuxing Hospital of Capital Medical University, Qingdao Municipal Hospital, Shengjing Hospital of China Medical University, Handan Central Hospital, the First Affiliated Hospital of Harbin Medical University, the Fourth Hospital of Hebei Medical University and General Hospital of Ningxia Medical University were consecutively included. A total of 24 pPCL patients were included with thirteen being male and eleven being female. The median age [M(Q1, Q3)] was 60 (57, 70) years. Patients were grouped according to peripheral blood plasma cell (PBPC) percentage [5%-19% (n=14) vs ≥20% (n=10)]. Last follow-up date was September 26th, 2023. The median follow-up period was 9.1 (4.2, 15.5) months. Patients' data related with clinical baseline characteristics, efficacy, survival and safety were retrospectively collected. Cox proportional hazards regression model was used to analyze risk factors associated with survival. Results: Among 24 pPCL patients, 16 (66.7%) patients had anemia at diagnosis, 13(54.2%) patients had thrombocytopenia, 8 (33.3%) patients had a baseline estimated glomerular filtration rate (eGFR)<40 ml·min-1·(1.73m2)-1, 13 (54.2%) patients had elevated lactate dehydrogenase (LDH) levels. The median PBPC percentage was 16% (8%, 26%) . Fluorescence in situ hybridization testing indicated that patients harboring 17p deletion, t(4;14) or t(14;16) were 6 (25.0%), 4 (16.7%) and 4 (16.7%), respectively. The overall response rate was 83.3% (20/24). The median progression-free survival (PFS) was 20.5 (95%CI: 15.8-25.2) months, and the median overall survival (OS) was not reached. Estimated 1-year and 2-year PFS and OS rates were 75.0% and 89.1%, 37.5% and 53.4%, respectively. The median PFS and OS for patients with PBPC percentages 5%-19% and≥20% were not reached and 20.5 (95%CI:15.7-25.3) months, 17.8 months and not reached, respectively. There was no significant statistical difference of PFS and OS between two groups (all P>0.05). Multivariate Cox regression analysis showed that 1p32 deletion was the risk factor associated with PFS (HR=7.7, 95%CI: 1.1-54.9, P=0.043). Seventeen patients (70.8%) developed grade 3-4 hematologic toxicities. Twelve patients (50.0%) developed grade 3-4 thrombocytopenia. Sixteen patients (66.7%) developed infection. All hematologic toxicities and infections were improved after supportive treatment. Conclusion: First-line treatment with anti-CD38 monoclonal antibody-based therapy for pPCL is effective and safe.

Interpretable CT radiomics model for invasiveness prediction in patients with ground-glass nodules

AIM

To evaluate the performance of an interpretable computed tomography (CT) radiomic model in predicting the invasiveness of ground-glass nodules (GGNs).

MATERIALS AND METHODS

The study was conducted retrospectively from 1 August 2017 to 1 August 2022, at three different centres. Two hundred and thirty patients with GGNs were enrolled at centre I as a training cohort. Centres II (n=157) and III (n=156) formed two external validation cohorts. Radiomics features extracted based on CT were reduced by a coarse-fine feature screening strategy. A radiomic model was developed through the use of the LASSO (least absolute shrinkage and selection operator) and XGBoost algorithms. Then, a radiological model was established through multivariate logistic regression analysis. Finally, the interpretability of the model was explored using SHapley Additive exPlanations (SHAP).

RESULTS

The radiomic XGBoost model outperformed the radiomic logistic model and radiological model in assessing the invasiveness of GGNs. The area under the curve (AUC) values for the radiomic XGBoost model were 0.885 (95% confidence interval [CI] 0.836-0.923), 0.853 (95% CI 0.790-0.906), and 0.838 (95% CI 0.773-0.902) in the training and the two external validation cohorts, respectively. The SHAP method allowed for both a quantitative and visual representation of how decisions were made using a given model for each individual patient. This can provide a deeper understanding of the decision-making mechanisms within the model and the factors that contribute to its prediction effectiveness.

CONCLUSIONS

The present interpretable CT radiomics model has the potential to preoperatively evaluate the invasiveness of GGNs. Furthermore, it can provide personalised, image-based clinical-decision support.

Comprehensive Time-Course Transcriptome Reveals the Crucial Biological Pathways Involved in the Seasonal Branch Growth in Siberian Elm (Ulmus pumila)

Timber, the most prevalent organic material on this planet, is the result of a secondary xylem emerging from vascular cambium. Yet, the intricate processes governing its seasonal generation are largely a mystery. To better understand the cyclic growth of vascular tissues in elm, we undertook an extensive study examining the anatomy, physiology, and genetic expressions in Ulmus pumila. We chose three robust 15-year-old elm trees for our study. The cultivars used in this study were collected from the Inner Mongolia Autonomous Region in China and nurtured in the tree farm of Shandong Normal University. Monthly samples of 2-year-old elm branches were taken from the tree from February to September. Marked seasonal shifts in elm branch vascular tissues were observed by phenotypic observation: In February, the cambium of the branch emerged from dormancy, spurring growth. By May, elms began generating secondary xylem, or latewood, recognized by its tiny pores and dense cell structure. From June to August, there was a marked increase in the thickness of the secondary xylem. Transcriptome sequencing provides a potential molecular mechanism for the thickening of elm branches and their response to stress. In February, the tree enhanced its genetic responses to cold and drought stress. The amplified expression of CDKB, CYCB, WOX4, and ARF5 in the months of February and March reinforced their essential role in the development of the vascular cambium in elm. Starting in May, the elm deployed carbohydrates as a carbon resource to synthesize the abundant cellulose and lignin necessary for the formation of the secondary wall. Major genes participating in cellulose (SUC and CESA homologs), xylan (UGD, UXS, IRX9, IRX10, and IRX14), and lignin (PAL, C4H, 4CL, HCT, C3H, COMT, and CAD) biosynthetic pathways for secondary wall formation were up-regulated by May or/and June. In conclusion, our findings provided a foundation for an in-depth exploration of the molecular processes dictating the seasonal growth of elm timber.

[Distribution and reference intervals of daytime intraocular pressure in the eye health screening population of Handan]

Objective: To describe the distribution and establish reference intervals (RI) of daytime intraocular pressure (IOP) in the eye health screening population of Handan. Methods: This cross-sectional study included subjects who participated in eye health screening at the Physical Examination Center of Handan First Hospital from May 2021 to June 2022. A complete general and ocular examination was performed, including measurements of visual acuity and IOP (using Goldmann tonometry), slit lamp microscopy, fundus photography, and anterior and posterior segment optical coherence tomography. Subjects with factors that could cause significant changes in IOP or affect the accuracy of IOP measurement, or with an inability to measure IOP were excluded. Simple random sampling was used to select participants, who were grouped by gender and age (18 to <30, 30 to <40, 40 to <50, 50 to <60, 60 to <70, and ≥70 years). Central corneal thickness and IOP at 8 to 11 o'clock in one eye of each participant were recorded. The independent sample t test and ANOVA were used for statistical analysis, and the RI of IOP values was calculated by x¯±1.96s. Results: A total of 9 310 subjects had their IOP measured, and 3 491 participants (3 491 eyes) were randomly selected from 7 886 healthy subjects. The age of the participants was (47.74±14.47) years old, ranging from 18 to 90 years old. There were 1 694 males and 1 797 females. The central corneal thickness of all participants was (525.56±49.39) μm. The daytime IOP of all participants was (15.40±2.54) mmHg (1 mmHg=0.133 kPa), and the RI was 10.42 to 20.39 mmHg. The IOP was (15.49±2.58) mmHg for males and (15.29±2.49) mmHg for females, and the gender difference was statistically significant (P<0.05). The RI of daytime IOP values was 10.43 to 20.54 mmHg for males and 10.41 to 20.18 mmHg for females. There were significant differences in daytime IOP [(15.13±2.58), (15.33±2.53), (15.49±2.50), (15.53±2.55), (15.39±2.62), and (15.28±2.52) mmHg] among 6 age groups (P<0.05). Conclusions: The distribution of daytime IOP in different gender and age groups in the eye health screening population of Handan and the RIs derived from the distribution were roughly the same as the international normal IOP RI (10 to 21 mmHg). It is recommended to refer to the RI of daytime IOP values of different genders and ages for clinical decision.

Plastid phylogenomics sheds light on divergence time and ecological adaptations of the tribe Persicarieae (Polygonaceae)

Southwestern China, adjacent to the Qinghai-Tibetan Plateau (QTP), is known as a hotspot for plant diversity and endemism, and it is the origin and diversification center of Persicarieae. As one of the major lineages in Polygonaceae, Persicarieae represents a diverse adaptation to various habitats. As a result of morphological plasticity and poorly resolving molecular markers, phylogenetic relationships and infrageneric classification within Persicarieae have long been controversial. In addition, neither plastome phylogenomic studies nor divergence time estimates on a larger sample of Persicarieae species have been made thus far. We sequenced and assembled 74 complete plastomes, including all of the recognized genera within Persicarieae and their relatives. We conducted a comprehensive phylogenetic study of the major clades within Persicarieae and, based on the thus obtained robust phylogeny, also estimated divergence time and the evolution of diagnostic morphological traits. Major relationships found in previous phylogenetic studies were confirmed, including those of the backbone of the tree, which had been a major problem in previous phylogenies of the tribe. Phylogenetic analysis revealed strong support for Koenigia as sister to Bistorta, and together they were sister to the robustly supported Persicaria. Based on the phylogenetic and morphological evidence, we recognize five sections in Persicaria: Persicaria, Amphibia, Tovara, Echinocaulon, and Cephalophilon. It is estimated that the divergence of the Persicarieae began around the late Paleocene, with diversification concentrated in the Eocene and Miocene. In addition, it is suggested that the increasing westerly and monsoon winds in conjunction with the uplift of the QTP may be the driving force for origin and diversification of Persicarieae species. These results provide a valuable evolutionary framework for the study of adaptation in Polygonaceae and insights into plant diversification on the QTP and adjacent areas.

Plastid phylogenomics and morphological character evolution of Chloridoideae (Poaceae)

Chloridoideae is one of the largest subfamilies of Poaceae, containing many species of great economic and ecological value; however, phylogenetic relationships among the subtribes and genera of Cynodonteae are controversial. In the present study, we combined 111 plastomes representing all five tribes, including 25 newly sequenced plastomes that are mostly from Cynodonteae. Phylogenetic analyses supported the five monophyletic tribes of Chloridoideae, including Centropodieae, Triraphideae, Eragrostideae, Zoysieae and Cynodonteae. Simultaneously, nine monophyletic lineages were revealed in Cynodonteae: supersubtribe Boutelouodinae, subtribes Tripogoninae, Aeluropodinae, Eleusininae, Dactylocteniinae, supersubtribe Gouiniodinae, Cleistogenes and Orinus, and subtribe Triodiinae. Within the tribe of Cynodonteae, the basal lineage is supersubtribe Boutelouodinae and Tripogoninae is sister to the remaining lineages. The clade formed of Aeluropodinae and Eleusininae is sister to the clade composed of Dactylocteniinae, supersubtribe Gouiniodinae, Cleistogenes and Orinus, and subtribe Triodiinae. The clade comprising Dactylocteniinae and supersubtribe Gouiniodinae is sister to the clade comprising Cleistogenes, Orinus, and Triodiinae. Acrachne is a genus within Eleusininae but not within Dactylocteniinae. Molecular evidence determined that Diplachne is not clustered with Leptochloa, which indicated that Diplachne should not be combined into Leptochloa. Cleistogenes is sister to a clade composed of Orinus and Triodia, whereas the recently proposed subtribe Orininae was not supported. Cynodonteae was estimated to have experienced rapid divergence within a short period, which could be a major obstacle in resolving its phylogenetic relationships. Ancestral state reconstructions of morphological characters showed that the most recent common ancestor (MRCA) of Chloridoideae has a panicle, multiple florets in each spikelet, the peaked type of stomatal subsidiary cells, and a saddle-shaped phytoliths, while the ancestral morphological characters of Cynodonteae are the panicle, peaked type of stomatal subsidiary cells, sharp-cap cell typed and equal-base-cell microhair, and square-shaped phytoliths. Overall, plastome phylogenomics provides new insights into the phylogenetic relationships and morphological character evolution of Chloridoideae.

Application of chloroplast genome in the identification of Traditional Chinese Medicine Viola philippica

BACKGROUND

Viola philippica Cav. is the only source plant of "Zi Hua Di Ding", which is a Traditional Chinese Medicine (TCM) that is utilized as an antifebrile and detoxicant agent for the treatment of acute pyogenic infections. Historically, many Viola species with violet flowers have been misused in "Zi Hua Di Ding". Viola have been recognized as a taxonomically difficult genera due to their highly similar morphological characteristics. Here, all common V. philippica adulterants were sampled. A total of 24 complete chloroplast (cp) genomes were analyzed, among these 5 cp genome sequences were downloaded from GenBank and 19 cp genomes, including 2 "Zi Hua Di Ding" purchased from a local TCM pharmacy, were newly sequenced.

RESULTS

The Viola cp genomes ranged from 156,483 bp to 158,940 bp in length. A total of 110 unique genes were annotated, including 76 protein-coding genes, 30 tRNAs, and four rRNAs. Sequence divergence analysis screening identified 16 highly diverged sequences; these could be used as markers for the identification of Viola species. The morphological, maximum likelihood and Bayesian inference trees of whole cp genome sequences and highly diverged sequences were divided into five monophyletic clades. The species in each of the five clades were identical in their positions within the morphological and cp genome tree. The shared morphological characters belonging to each clade was summarized. Interestingly, unique variable sites were found in ndhF, rpl22, and ycf1 of V. philippica, and these sites can be selected to distinguish V. philippica from samples all other Viola species, including its most closely related species. In addition, important morphological characteristics were proposed to assist the identification of V. philippica. We applied these methods to examine 2 "Zi Hua Di Ding" randomly purchased from the local TCM pharmacy, and this analysis revealed that the morphological and molecular characteristics were valid for the identification of V. philippica.

CONCLUSIONS

This study provides invaluable data for the improvement of species identification and germplasm of V. philippica that may facilitate the application of a super-barcode in TCM identification and enable future studies on phylogenetic evolution and safe medical applications.

Plastid and mitochondrial phylogenomics reveal correlated substitution rate variation in Koenigia (Polygonoideae, Polygonaceae) and a reduced plastome for Koenigia delicatula including loss of all ndh genes

Koenigia, a genus proposed by Linnaeus, has a contentious taxonomic history. In particular, relationships among species and the circumscription of the genus relative to Aconogonon remain uncertain. To explore phylogenetic relationships of Koenigia with other members of tribe Persicarieae and to establish the timing of major evolutionary diversification events, genome skimming of organellar sequences was used to assemble plastomes and mitochondrial genes from 15 individuals representing 13 species. Most Persicarieae plastomes exhibit a conserved structure and content relative to other flowering plants. However, Koenigia delicatula has lost functional copies of all ndh genes and the intron from atpF. In addition, the rpl32 gene was relocated in the K. delicatula plastome, which likely occurred via overlapping inversions or differential expansion and contraction of the inverted repeat. The highly supported but conflicting relationships between plastome and mitochondrial trees and among gene trees complicates the circumscription of Koenigia, which could be caused by rapid diversification within a short period. Moreover, the plastome and mitochondrial trees revealed correlated variation in substitution rates among Persicarieae species, suggesting a shared underlying mechanism promoting evolutionary rate variation in both organellar genomes. The divergence of dwarf K. delicatula from other Koenigia species may be associated with the well-known Eocene Thermal Maximum 2 or Early Eocene Climatic Optimum event, while diversification of the core-Koenigia clade associates with the Mid-Miocene Climatic Optimum and the uplift of Qinghai-Tibetan Plateau and adjacent areas.

Characterization of the complete chloroplast genome of Achnatherum pekinense (Poaceae), a widespread weed

Achnatherum pekinense belongs to Poaceae. The complete chloroplast genome of A. pekinense was reported in this study. The chloroplast genome was 137,837 bp in size with a canonical quadripartite structure, including two inverted repeat regions (IR) of 21,635 bp for each, a large single-copy (LSC) region of 81,787 bp in length, and a small single-copy (SSC) region of 12,780 bp in length. The overall guanine-cytosine (GC) content of this chloroplast genome was 38.8%, and the corresponding values of the LSC, SSC, and IR regions were 36.9%, 33.1%, and 44.1%, respectively. A total of 113 unique genes were annotated in this chloroplast genome, including four rRNA genes, 31 tRNA genes, and 78 protein-coding genes. The phylogenetic analysis showed that A. pekinense was clustered with A. inebrians.

Comprehensive Time-Course Transcriptome and Co-expression Network Analyses Identify Salt Stress Responding Mechanisms in Chlamydomonas reinhardtii Strain GY-D55

It is highly necessary to understand the molecular mechanism underlying the salt stress response in green algae, which may contribute to finding the evolutionary cues of abiotic stress response in plants. Here, we reported a comprehensive temporal investigation of transcriptomes using data at eight different time points, from an early stage (2 h) to a late stage (up to 96 h) in Chlamydomonas reinhardtii GY-D55 cells. The principal component analysis (PCA) of transcriptome profiles showed that the samples of the early and late stages were well separated. A total of 12,445 genes were detected as differentially expressed genes. There were 1,861/2,270 common upregulated/downregulated genes for each time point compared with control samples. Samples treated with salt for 2, 8, and 24 h had a relatively large number of characteristic upregulated/downregulated genes. The functional enrichment analysis highlighted the timing of candidate regulatory mechanisms for salt stress responses in GY-D55 cells. Short time exposure to salt stress impaired oxidation-reduction, protein synthesis and modification, and photosynthesis. The algal cells promoted transcriptional regulation and protein folding to deal with protein synthesis/modification impairments and rapidly accumulated glycerol in the early stage (2-4 h) to cope with osmotic stress. At 12 and 24 h, GY-D55 cells showed increased expressions of signaling and photosynthetic genes to deal with the damage of photosynthesis. The co-expression module blue was predicted to regulate endoplasmic reticulum (ER) stress at early time points. In addition, we identified a total of 113 transcription factors (TFs) and predicted the potential roles of Alfin, C2C2, and the MYB family TFs in algal salt stress response.

A Novel Alginate Lyase: Identification, Characterization, and Potential Application in Alginate Trisaccharide Preparation

Alginate oligosaccharides (AOS) have many biological activities and significant applications in prebiotics, nutritional supplements, and plant growth development. Alginate lyases have unique advantages in the preparation of AOS. However, only a limited number of alginate lyases have been so far reported to have potentials in the preparation of AOS with specific degrees of polymerization. Here, an alginate-degrading strain Pseudoalteromonasarctica M9 was isolated from Sargassum, and five alginate lyases were predicted in its genome. These putative alginate lyases were expressed and their degradation products towards sodium alginate were analyzed. Among them, AlyM2 mainly generated trisaccharides, which accounted for 79.9% in the products. AlyM2 is a PL6 lyase with low sequence identity (≤28.3%) to the characterized alginate lyases and may adopt a distinct catalytic mechanism from the other PL6 alginate lyases based on sequence alignment. AlyM2 is a bifunctional endotype lyase, exhibiting the highest activity at 30 °C, pH 8.0, and 0.5 M NaCl. AlyM2 predominantly produces trisaccharides from homopolymeric M block (PM), homopolymeric G block (PG), or sodium alginate, with a trisaccharide production of 588.4 mg/g from sodium alginate, indicating its promising potential in preparing trisaccharides from these polysaccharides.

Comparative and Phylogenetic Analysis of Complete Plastomes among Aristidoideae Species (Poaceae)

Aristidoideae is a subfamily in the PACMAD clade of family Poaceae, including three genera, Aristida, Stipagrostis, and Sartidia. In this study, the plastomes of Aristida adscensionis and Stipagrostis pennata were newly sequenced, and a total of 16 Aristidoideae plastomes were compared. All plastomes were conservative in genome size, gene number, structure, and IR boundary. Repeat sequence analysis showed that forward and palindrome repeats were the most common repeat types. The number of SSRs ranged from 30 (Sartidia isaloensis) to 54 (Aristida purpurea). Codon usage analysis showed that plastome genes preferred to use codons ending with A/T. A total of 12 highly variable regions were screened, including four protein coding sequences (matK, ndhF, infA, and rpl32) and eight non-coding sequences (rpl16-1-rpl16-2, ccsA-ndhD, trnY-GUA-trnD-GUC, ndhF-rpl32, petN-trnC-GCA, trnT-GGU-trnE-UUC, trnG-GCC-trnfM-CAU, and rpl32-trnL-UAG). Furthermore, the phylogenetic position of this subfamily and their intergeneric relationships need to be illuminated. All Maximum Likelihood and Bayesian Inference trees strongly support the monophyly of Aristidoideae and each of three genera, and the clade of Aristidoideae and Panicoideae was a sister to other subfamilies in the PACMAD clade. Within Aristidoideae, Aristida is a sister to the clade composed of Stipagrostis and Sartidia. The divergence between C₄&nbsp;Stipagrostis and C₃&nbsp;Sartidia was estimated at 11.04 Ma, which may be associated with the drought event in the Miocene period. Finally, the differences in carbon fixation patterns, geographical distributions, and ploidy may be related to the difference of species numbers among these three genera. This study provides insights into the phylogeny and evolution of the subfamily Aristidoideae.

Characterization and phylogenetic analysis of the complete plastome of Amaranthus retroflexus L. (Amaranthaceae), an annual weeds

The complete plastome of Amaranthus retroflexus L., a field weed, was identified in this study. The genome size was 150,710 bp and consists of a large single-copy (LSC: 83,892 bp) region, a small single-copy (SSC: 18,100 bp) region, and two inverted repeats (IRs: 24,359 bp) regions. GC content was 36.6%. A total of 113 genes were identified, including 79 protein-coding genes, four rRNA genes, and 30 tRNA genes. Twenty chloroplast genomes from Amaranthaceae were selected to reconstruct phylogenetic tree and the result supported that A. retroflexus was sister to A. hypochondriacus and A. caudatus.

Characterization and phylogenetic analysis of the complete plastome of Veronica undulata (Plantaginaceae)

Veronica undulata is a perennial herb, and the complete chloroplast genome (plastome) of V. undulata was determined in this study. The results showed that the plastome size of V. undulata was 151,178 bp, including a large single-copy region (68,533 bp), a small single-copy region (21,403 bp), and two inverted repeat regions (25,566 bp). The total GC content of the plastome was 38.1%. We annotated 115 unique genes in the plastome, including 81 protein-coding genes (PCGs), 30 tRNAs, and four rRNAs. Phylogenetic analysis showed that the species of V. undulata and Veronica clustered together.

Characterization and phylogenetic analysis of the complete chloroplast genome of Amaranthus viridis (Amaranthaceae)

Amaranthus viridis is an important medicinal herb. In this study, the complete chloroplast genome (plastome) of A. viridis was repotred. It was a circular molecular of 150,452 bp in length and consists of a large single-copy region (LSC, 83,832 bp), a small single-copy region (SSC, 17,914 bp), and two inverted repeats (IRs, 24,353 bp for each) regions. The overall GC content was 36.6%. This plastome encodes 113 unique genes, including 79 protein-coding genes, 30 tRNAs, and four rRNAs. The phylogenetic tree of 18 Amaranthaceae chloroplast genomes supported that A. viridis was closely related to A. hybridus.

Comparative Plastomes and Phylogenetic Analysis of Cleistogenes and Closely Related Genera (Poaceae)

Cleistogenes (Orininae, Cynodonteae, Chloridoideae, Poaceae) is an ecologically important genus. The phylogenetic placement of Cleistogenes and phylogenetic relationships among Cleistogenes taxa remain controversial for a long time. To resolve the intra- and inter-generic relationships of Cleistogenes, the plastomes of 12 Cleistogenes taxa (including 8 species and 4 varieties), one Orinus species, 15 Triodia species, two Tripogon species, and two Aeluropus species were included in the present study. All the taxa showed a similar pattern in plastome structure, gene order, gene content, and IR boundaries. The number of simple sequence repeats ranged from 145 (O. kokonorica) to 161 (T. plurinervata and T. schinzii). Moreover, 1,687 repeats were identified in these taxa, including 1,012 forward, 650 palindromic, 24 reverse, and one complement. Codon usage analysis revealed that these plastomes contained 16,633 (T. stipoides) to 16,678 (T. tomentosa) codons. Sequence divergence analysis among Cleistogenes and closely related genera identified five non-coding regions (trnS-UGA-psbZ, rpl32-trnL-UAG, trnQ-UUG-psbK, trnD-GUC-psbM, trnT-GGU-trnE-UUC). Phylogenetic analysis of complete plastomes indicated that Cleistogenes is sister to a clade composed of Orinus and Triodia, whereas it did not support the sister relationship between the recently proposed subtribe Orininae (Cleistogenes and Orinus) and Triodia. The subtribe Orininae was not supported by our complete plastome data. The split between Cleistogenes and Orinus-Triodia clade go back to 14.01 Ma. Besides, our findings suggested that C. squarrosa and C. songorica are the successive early diverging groups in the phylogenetic analysis. The other 10 taxa are divided into two groups: a monophyletic group composed of Cleistogenes sp. nov. and C. caespitosa var. ramosa is sister to other eight Cleistogenes taxa. Cleistogenes was estimated to have experienced rapid divergence within a short period, which could be a major obstacle in resolving phylogenetic relationships within Cleistogenes. Collectively, our results provided valuable insights into the phylogenetic study of grass species.

Characterization of the complete plastome of Aster pekinensis (Asteraceae), a perennial herb

Aster pekinensis is a perennial herb that distributes widely in China, Korea, and Eeastern Russia. The complete plastome of A. pekinensis is reported here. It is a circular molecular of 152,815 bp in length and consists of a large single-copy region (LSC: 84,530 bp), a small single-copy region (SSC: 18,219 bp), and two inverted repeats (IR: 25,033 bp) regions. GC content is 37.3%. This plastome encodes 113 unique genes, including 79 protein-coding genes, 30 tRNAs, and 4 rRNAs. Phylogenomic analysis of 17 plastomes within Aster and closely related genera revealed that A. pekinensis was sister to the clade comprising A. flaccidus and A. altaicus.

Marinomonas algicola sp. nov. and Marinomonas colpomeniae sp. nov., isolated from marine macroalgae

Two Gram-stain-negative, aerobic, rod-shaped bacteria, polar flagellated, designated strains SM2066^T and SM1966^T, were respectively isolated from the surfaces of Colpomenia sinuosa and Ulva pertusa macroalgae collected off the coastal areas of Rongcheng, PR China. Strain SM2066^T grew at 8-37 °C and with 0.5-7.0 % (w/v) NaCl, while strain SM1966^T grew at 5-30 °C and with 0.5-8.5% (w/v) NaCl. Both of them reduced nitrate to nitrite and required Na⁺ for growth but neither of them hydrolysed starch and DNA. Phylogenetic analysis based on 16S rRNA gene and single-copy orthologous cluster sequences revealed that both strains SM2066^T and SM1966^T were affiliated with the genus Marinomonas but formed distinct phylogenetic branches from known Marinomonas species, respectively sharing the highest 16S rRNA gene sequence similarities with type strains of Marinomonas ushuaiensis (97.9 %) and Marinomonas blandensis (96.7 %). The digital DNA-DNA hybridization and average nucleotide identity values between strains SM2066^T and SM1966^T and type strains of closely related Marinomonas species were all below 22.9 and 79.9 mol%, respectively. The major fatty acids of the two strains were summed feature 3 (C_16 : 1  ω6c/C_16 : 1  ω7c), summed feature 8 (C_18 : 1  ω7c) and C_16 : 0, with their predominant polar lipids being phosphatidylethanolamine and phosphatidylglycerol, and their sole respiratory quinone being Q-8. The genomic DNA G+C contents of strains SM2066^T and SM1966^T determined from genomic sequences were 40.3 and 41.6 mol%, respectively. On the basis of the polyphasic evidence presented in this study, strains SM2066^T and SM1966^T are considered to represent two novel species within the genus Marinomonas, for which the names Marinomonas colpomeniae sp. nov. and Marinomonas algicola sp. nov. are proposed. The type strains are SM2066^T (=MCCC 1K04390^T= KCTC 82372^T) and SM1966^T (=MCCC 1K04387^T= KCTC 72848^T), respectively.

Comparative and Phylogenetic Analysis of Complete Chloroplast Genomes in Eragrostideae (Chloridoideae, Poaceae)

Eragrostideae Stapf, the second-largest tribe in Chloridoideae (Poaceae), is a taxonomically complex tribe. In this study, chloroplast genomes of 13 Eragrostideae species were newly sequenced and used to resolve the phylogenetic relationships within Eragrostideae. Including seven reported chloroplast genomes from Eragrostideae, the genome structure, number and type of genes, codon usage, and repeat sequences of 20 Eragrostideae species were analyzed. The length of these chloroplast genomes varied from 130,773 bp to 135,322 bp. These chloroplast genomes showed a typical quadripartite structure, including a large single-copy region (77,993–80,643 bp), a small single-copy region (12,410–12,668 bp), and a pair of inverted repeats region (19,394–21,074 bp). There were, in total, 129–133 genes annotated in the genome, including 83–87 protein-coding genes, eight rRNA genes, and 38 tRNA genes. Forward and palindromic repeats were the most common repeat types. In total, 10 hypervariable regions (rpl22, rpoA, ndhF, matK, trnG–UCC-trnT–GGU, ndhF–rpl32, ycf4–cemA, rpl32–trnL–UAG, trnG–GCC–trnfM–CAU, and ccsA–ndhD) were found, which can be used as candidate molecular markers for Eragrostideae. Phylogenomic studies concluded that Enneapogon diverged first, and Eragrostis including Harpachne is the sister to Uniola. Furthermore, Harpachne harpachnoides is considered as a species of Eragrostis based on morphological and molecular evidence. In addition, the interspecies relationships within Eragrostis are resolved based on complete chloroplast genomes. This study provides useful chloroplast genomic information for further phylogenetic analysis of Eragrostideae.

First report of the parasitic invasive weed field dodder (Cuscuta campestris) parasitizing the confamilial invasive weed common morning-glory (Ipomoea purpurea) in Shandong, China

Common morning-glory (Ipomoea purpurea (L.) Roth, Convolvulaceae), an annual herbaceous vine native to South America, was first recorded to be cultivated in China in 1890, and since then it has invaded all provinces of China. It was one of the 18 alien invasive species in China (MEE. 2014). As an invasive weed, it can readily invade dry lands, orchards, and nurseries and compete for sunlight by wrapping other plants. On 20 September 2019 and 18 July 2020, I. purpurea was found to be parasitized by a dodder species (also Convolvulaceae) in Lushan Mountain (36°21'N, 118°3'E, 569 m elevation), Shandong province, China (Fig. S1). Within and area of ca. 100 m2, dozens of individuals of common morning-glory were parasitized by the leafless stems of dodder. After removal of the haustrial connection of the dodder stem from the I. purpurea stem, brownish black lesions around uneven holes were visible on the I. purpurea stem, with broken haustoria clearly visible to our naked eye remaining in the I. purpurea stem (Fig. S1). Anatomical results showed that the haustoria of dodder penetrate I. purpurea stem and xylem elements connect the vascular systems of both the parasitic and host plant (Fig. S1). Based on morphological characteristics of stems, inflorescences, calyx, corolla, stamens, and capsules as described in Costea et al. (2006), this dodder was identified as Cuscuta campestris Yunck. (i.e., field dodder). Field dodder is readily distinguished from C. chinensis and C. australis in China by the capsules with persistent corollas enveloping 1/3 or less of its base and the spreading and inflexed corolla lobes with acute to acuminate apices. In order to further confirm the identity of the species, total genomic DNA was extracted and sequenced using genome-skimming method as described in Qu et al. (2019). An 831-bp region of 18S-ITS1-5.8S-ITS2-26S for the dodder studied was assembled, examined, and deposited in GenBank under accession number MN718805. The new sequence has 100% similarity with other available sequences of C. campestris (accession number: KT383104, KT383150, KY968857). Phylogenetic analysis also placed the new dodder accession with other accessions of C. campestris (Fig. S2a). In addition, the plastome sequence of the dodder studied was assembled (86,727 bp in length) and deposited in GenBank under accession number MN708214, and a BLAST analysis found that it was 99.98% similar to that of C. gronovii (accession number: AM711639). The plastome of C. gronovii was published by Funk et al. (2007). However, Costea et al. (2015) indicated that Funk et al. (2007) misidentified C. campestris as C. gronovii. Furthermore, our phylogenetic tree strongly supported the identification of the dodder studied as C. campestris (Fig. S2b). Therefore, the dodder on common morning-glory in Shandong province was finally identified as C. campestris according to morphological and molecular evidence. The specimen of C. campestris on I. purpurea was deposited at the herbarium of the College of Life Sciences, Shandong Normal University (voucher number: 092012B). Field dodder, the second most common dodder species in North America, is the most widespread Cuscuta weed in the world and has been found in Africa, Asia, Australia, Europe, and South America (Holm et al. 1997). To our knowledge, this is the first report of the parasitic invasive weed C. campestris parasitizing the invasive weed I. purpurea in Shandong of China. This is also the first report of Cuscuta species parasitizing confamilial Ipomoea species, which is especially noteworthy given that the genus Cuscuta is sister to the genus Ipomoea. This study provides a good model for exploring gene flow between species of closely related genera with different lifestyle. Another implication of this study is that customs and departments of inspection and quarantine need to quarantine the seeds or plants of both dodders and common morning-glories.

Marinomonas profundi sp. nov., isolated from deep seawater of the Mariana Trench

A Gram-stain-negative, aerobic, polarly flagellated, straight or curved rod-shaped bacterium, designated strain M1K-6^T, was isolated from deep seawater samples collected from the Mariana Trench. The strain grew at -4 to 37 °C (optimum, 25-30 °C), at pH 5.5-10.0 (optimum, pH 7.0) and with 0.5-14.0  % (w/v) NaCl (optimum, 2.0 %). It did not reduce nitrate to nitrite nor hydrolyse gelatin or starch. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain M1K-6^T was affiliated with the genus Marinomonas, sharing 93.1-97.0  % sequence similarity with the type strains of recognized Marinomonas species. The major cellular fatty acids were summed feature 3 (C_16 : 1 ω6c/C_16 : 1 ω7c), summed feature 8 (C_18 : 1 ω7c/C_18 : 1 ω6c), C_16 : 0, C_10 : 0 3-OH and C_18 : 0. The predominant respiratory quinone was ubiquinone-8. Polar lipids of strain M1K-6^T included phosphatidylethanolamine, phosphatidylglycerol and two unidentified lipids. The genomic G+C content of strain M1K-6^T was 46.0 mol%. Based on data from the present polyphasic study, strain M1K-6^T was considered to represent a novel species within the genus Marinomonas, for which the name Marinomonas profundi sp. nov. is proposed. The type strain is M1K-6^T (=KCTC 72501^T=MCCC 1K03890^T).

Characterization of the complete chloroplast genome of Rumex nepalensis (Polygonaceae)

Rumex nepalensis (Polygonaceae) is a fairly common perennial herb of high altitudes. In this study, we determined the complete chloroplast genome (plastome) of R. nepalensis with genome-skimming method. The complete plastome of R. nepalensis was 159,110 bp in length with a quadripartite structure, including a large single-copy region of 84,810 bp, a small single-copy region of 13,044 bp, and a pair of inverted repeats regions of 30,628 bp. The overall guanine-cytosine (GC) content was 37.5%. A total of 112 unique genes was annotated in this plastome, including 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. In the ML tree, R. nepalensis was sister to R. crispus, and Rumex was sister to a clade comprising Rheum and Oxyria within Polygonaceae famliy.

Comparative Transcriptome Analysis of Halophyte Zoysia macrostachya in Response to Salinity Stress

As one of the most severe environmental stresses, salt stress can cause a series of changes in plants. In salt tolerant plant Zoysia macrostachya, germination, physiology, and genetic variation under salinity have been studied previously, and the morphology and distribution of salt glands have been clarified. However, no study has investigated the transcriptome of such species under salt stress. In the present study, we compared transcriptome of Z. macrostachya under normal conditions and salt stress (300 mmol/L NaCl, 24 h) aimed to identify transcriptome responses and molecular mechanisms under salt stress in Z. macrostachya. A total of 8703 differently expressed genes (DEGs) were identified, including 4903 up-regulated and 3800 down-regulated ones. Moreover, a series of molecular processes were identified by Gene Ontology (GO) analysis, and these processes were suggested to be closely related to salt tolerance in Z. macrostachya. The identified DEGs concentrated on regulating plant growth via plant hormone signal transduction, maintaining ion homeostasis via salt secretion and osmoregulatory substance accumulation and preventing oxidative damage via increasing the activity of ROS (reactive oxygen species) scavenging system. These changes may be the most important responses of Z. macrostachya under salt stress. Some key genes related to salt stress were identified meanwhile. Collectively, our findings provided valuable insights into the molecular mechanisms and genetic underpinnings of salt tolerance in Z. macrostachya.

Characterization of the complete plastome of Alopecurus aequalis (Poaceae), a widespread weed

Alopecurus aequalis is a predominant weed species that distributes widely in North temperate regions. The complete plastome of A. aequalis is reported here. It is a circular molecular of 136,382 bp in length and consists of a large single-copy region (LSC: 80,455 bp), a small single-copy region (SSC: 12,849 bp), and two inverted repeats regions (IRs: 21,539 bp). GC content is 38.3%. This plastome encodes 112 unique genes, including 78 protein-coding genes, 30 tRNAs, and 4 rRNAs. Phylogenetic tree shows that A. aequalis is sister to Poa annua.

Characterization of the complete chloroplast genome of an annual halophyte, Chenopodium glaucum (Amaranthaceae)

The complete chloroplast genome (plastome) of Chenopodium glaucum, an annual halophytic herb, was determined. The plastome was 152,191 bp in size, containing a large single-copy region (83,675 bp), a small single-copy region (18,130 bp), and two inverted repeats regions (25,193 bp). The overall GC content of this plastome was 37.2%. In total, 113 unique genes were annotated including 79 protein-coding genes (PCGs), 30 tRNAs and 4 rRNAs. Phylogenomic analysis showed that C. glaucum was sister to C. album.

Plastome Reduction in the Only Parasitic Gymnosperm Parasitaxus Is Due to Losses of Photosynthesis but Not Housekeeping Genes and Apparently Involves the Secondary Gain of a Large Inverted Repeat

Plastid genomes (plastomes) of parasitic plants undergo dramatic reductions as the need for photosynthesis relaxes. Here, we report the plastome of the only known heterotrophic gymnosperm Parasitaxus usta (Podocarpaceae). With 68 unique genes, of which 33 encode proteins, 31 tRNAs, and four rRNAs in a plastome of 85.3-kb length, Parasitaxus has both the smallest and the functionally least capable plastid genome of gymnosperms. Although the heterotroph retains chlorophyll, all genes for photosynthesis are physically or functionally lost, making photosynthetic energy gain impossible. The pseudogenization of the three plastome-encoded light-independent chlorophyll biosynthesis genes chlB, chlL, and chlN implies that Parasitaxus relies on either only the light-dependent chlorophyll biosynthesis pathway or another regulation system. Nesting within a group of gymnosperms known for the absence of the large inverted repeat regions (IRs), another unusual feature of the Parasitaxus plastome is the existence of a 9,256-bp long IR. Its short length and a gene composition that completely differs from those of IR-containing gymnosperms together suggest a regain of this critical, plastome structure-stabilizing feature. In sum, our findings highlight the particular path of lifestyle-associated reductive plastome evolution, where structural features might provide additional cues of a continued selection for plastome maintenance.

Arabidopsis MDN1 Is Involved in the Establishment of a Normal Seed Proteome and Seed Germination

Seed germination and formation are the beginning and ending, respectively, of a plant life cycle. These two processes are under fine regulation by the internal genetic information. Previously, we demonstrated that Arabidopsis MIDASIN 1 (MDN1) is required for ribosome biogenesis, and its dysfunction leads to pleiotropic developmental phenotypes, including impaired embryogenesis and slow seed germination. In this study, we further found that the weak mutant of MDN1, mdn1-1, exhibits an increased seed size phenotype. Seed proteomic analysis reveals that a number of proteins involved in seed development and response to external environments are mis-regulated by the MDN1 dysfunction. Many 2S seed storage proteins (SSPs) and late embryogenesis abundant (LEA) proteins are over-accumulated in the dry seeds of mdn1-1. Further, some genes encoding seed storage reserves are also upregulated in mdn1-1 seedlings. More interestingly, abscisic acid-insensitive 5 (ABI5) is over-accumulated in mdn1-1 seeds, and the loss of its function partially rescues the low seed germination rate of mdn1-1. Together, this study further demonstrates that MDN1 is essential for establishing a normal seed proteome, and its mutation triggers ABI5-mediated repression of seed germination.

The complete chloroplast genome of an annual halophyte herb, Suaeda glauca (Amaranthaceae)

The complete chloroplast genome (plastome) of Suaeda glauca, an annual halophytic herb, was determined in this study. The plastome was 149,807 bp in size, containing a large single-copy region (82,162 bp), a small single-copy region (18,191 bp), and two inverted repeats regions (24,727 bp). The overall GC content of this plastome was 36.5%. In total, 113 unique genes, including 79 protein-coding genes (PCGs), 30 tRNAs and 4 rRNAs, were annotated. Phylogenomic analysis showed that S. glauca was sister to other Suaeda species.

Characterization of the complete plastome of Atriplex centralasiatica (Chenopodiaceae), an annual halophytic herb

Atriplex centralasiatica, an annual halophytic herb, is one of the most important Chinese herbal medicines, forages and indicator plants for saline-alkali soil. In this study, we report the complete plastome of A. centralasiatica. The plastome was 152,237 bp in length and comprises a large single-copy region (83,721 bp), a small single-copy region (18,096 bp), and a pair of inverted repeats (25,210 bp). It encodes 113 unique genes, including 79 protein-coding genes (PCGs), 30 tRNAs and 4 rRNAs. The overall GC content of this plastome was 37.3%. Phylogenomic analysis based on 21 plastomes revealed that A. centralasiatica was closely related to the genus Chenopodium.

Characterization of the complete chloroplast genome of Suaeda salsa (Amaranthaceae/Chenopodiaceae), an annual succulent halophyte

Suaeda salsa, an annual succulent halophytic herb, is one of the major halophyte widely distributed in both saline inland and the intertidal zone. In this study, we report the complete chloroplast genome (plastome) of S. salsa. The plastome was 151,642 bp in length and comprises a large single-copy region (83,502 bp), a small single-copy region (17,780 bp), and a pair of inverted repeats (25,180 bp). It encodes 113 unique genes, including 79 protein-coding genes (PCGs), 30 tRNAs, and four rRNAs. The overall GC content of this plastome was 36.4%. Phylogenomic analysis based on 20 plastomes revealed that S. salsa was closely related to S. malacosperma.

Sources of formaldehyde and their contributions to photochemical O3 formation at an urban site in the Pearl River Delta, southern China

Two models (the Positive Matrix Factorization (PMF) model and a photochemical box model with Master Chemical Mechanism (PBM-MCM)) were applied to analyze the formaldehyde (HCHO) data collected in July 2006 at an urban site (GPEMC) in the Pearl River Delta (PRD), southern China. Three major HCHO sources (secondary formation, vehicular exhaust, and solvent usage) were identified and they were found to contribute in average 53%, 31% and 16% respectively to the total HCHO loading at GPEMC. Alkenes was the most important group contributing to the secondary formation of HCHO, followed by aromatics and alkanes. Among them, trans-2-butene had the largest contribution to secondary HCHO formation, with the average percentage of 16 ± 4%, followed by i-butene, cis-2-butene, propene, isoprene and m,p-xylene. Secondary HCHO and HCHO emitted from vehicular emissions contributed comparably to ground-based measured O₃ and HO_x radical at GPEMC, higher than that from solvent usage (1.3 ± 0.1 ppbv and (4.1 ± 0.3) × 10⁶ molecule/cm³ for O₃ and HO_x radical). Our results highlight the importance of secondary HCHO formation for both photochemical formation of ozone and the oxidative capacity of the atmosphere in this region. It is hence critical for policy makers to propose strategies for controlling VOCs from vehicular emissions in order to reduce secondary HCHO formation. Our results also have important implication for improving the understanding of the source apportionments of HCHO and their contributions to photochemical pollution in the PRD region in China.

Genetic diversity of wild soybean populations in Dongying, China, by simple sequence repeat analysis

Annual wild soybean (Glycine soja Sieb. et Zucc.), the ancestor of cultivated soybean (G. max), is believed to be a potential gene source for further improvement of soybean to cope with environmental stress. In this study, 10 simple sequence repeat (SSR) markers were used to evaluate the genetic diversity and population genetic structure in five wild soybean populations using 195 accessions collected from Dongying, China. Ten SSR markers yielded 90 bands, with an average of nine bands per marker. The percentage of polymorphic loci (P) was 97.78%, the distribution of expected heterozygosity (HE) was 0.1994-0.4460 with an average of 0.3262, and the distribution from Shannon's information index (I) was 0.3595-0.6506 with an average of 0.5386. The results showed that wild soybean had a high degree of genetic diversity at the species level. Nei's differentiation coefficient (FST) was 0.1533, and gene flow (Nm) was 1.3805, which indicated that genetic variation mainly existed within populations and that there was a certain level of gene exchange between populations. Some genetic differentiation occurred among populations, although this was not significant. Cluster analysis indicated that there was no significant correlation between the genetic structure of wild soybean populations and their geographic distribution, and the clustering results may be relatively consistent with the habitats of the accessions. In the present study, the genetic diversity of wild soybeans showed a broad genetic base and enables suggestions for the conservation of this plant to be made.

An improved CTAB-ammonium acetate method for total RNA isolation from cotton

INTRODUCTION

Cotton is an important economic crop. Genetic, developmental and molecular studies of cotton require high-quality total RNA from different tissues. Due to the richness in polyphenols and polysaccharides, the Trizol-based methods and other commercial kits are unsuitable for RNA isolation from cotton. Available methods are generally laborious and time-consuming.

OBJECTIVE

To develop an easy, simple and rapid cetyltrimethylammonium bromide (CTAB)-ammonium acetate protocol that takes less time and obtains high yield and quality of RNA from polysaccharide- and polyphenol-rich cotton tissues.

METHODOLOGY

Based on the original CTAB protocol, we used phenol-chloroform and chloroform-isoamyl alcohol to remove proteins, polysaccharides and polyphenols, and ammonium acetate to precipitate RNA, reducing the incubation time prior to RNA precipitation. After adding ammonium acetate to precipitate RNA, all centrifugation steps (14000 × g) were carried out at 4°C to avoid degradation.

RESULTS

The procedure took only 1.5 h and was suitable for different cotton tissues. The A(260) : A(280) ratios ranged from 1.80 to 1.85 with clear 28 s and 18 s ribosomal RNA bands in 1.2% agarose gel. The isolated RNA was usable for downstream molecular studies, such as reverse transcription polymerase chain reaction (PCR) and real-time quantitative PCR.

CONCLUSION

The CTAB-ammonium acetate method is easy, rapid, low-cost and effective for high-quality RNA isolation from polysaccharide- and polyphenol-rich cotton tissues.

Knockdown of RhoGDIα induces apoptosis and increases lung cancer cell chemosensitivity to paclitaxel

This study aimed to investigate the effects of RhoGDIα knockdown on apoptosis and the chemosensitivity of lung cancer cells to paclitaxel. The signaling proteins involved were also assessed. RhoGDIα expression was assessed by RT-PCR, Western blotting and immunohistochemistry. Apoptosis was determined by flow cytometric assessment, and cell viability was measured with the MTT assay. Phosphorylation levels of signaling proteins, ERK, JNK, Akt, Bad and IκBα were tested by Western blotting and immunohistochemistry. Positivity for RhoGDIα in lung cancer tissues was significantly higher than in paracancerous tissues. Downregulation of RhoGDIα was associated with significantly increased apoptosis and repressed cell viability. This effect could be due to the consequent upregulation of p-JNK, as well as decreased levels of p-ERK, p-Bad and p-IκBα. Knockdown of RhoGDIα strengthened the effect on apoptosis and inhibition of cell viability induced by paclitaxel treatment. This chemosensitization effect could be a result of the intensification of pro-apoptotic JNK activation, and repression of anti-apoptotic p-ERK, p-Bad and p-IκBα expression stimulated by paclitaxel. In summary, our study indicated that RhoGDIα could be a promising therapeutic target, and the combination of RhoGDIα siRNA and paclitaxel might be a valuable potential therapy for lung cancer treatment.

[Analyses of chromosomal karyotypes and cytogenetic variations of animal cell lines]

After the master cell stock(mcs) and working cell bank of more than 30 different strains of 7 animal kidney cell lines (F-81 or CRFK cell line, MDCK cell line, Vero or Vero-2 cell line, MA-104 cell line and BHK-21 cell line) were established in China, the chromosomal number variations and structural aberrations of the above lines, primary feline or canine kidney cell (FKC or CKC) and HeLa cell line were investigated and their karyotypes of routine or Giemsa chromosomal bands were analyzed. The carcinogenesis or tumorigenicity testing of these cells in about 700 nude mice and for colony formation in soft agar (SA) and for agglutination under different concentration of plant lectins was carried out. Both tumorigenicity-negative strains of F-81, CRFK, Vero or Vero-2 lines and very-low-tumorigenicity strains of MDCK line were successfully selected and evaluated for the production of canine or feline combination viral vaccines, which are free of infectious agents, and described with respect to cytogenetic characteristics and tumorigenicity. Rate of modal chromosome number represents the ratio of cell number having modal chromosome number to all the split cell number analyzed at random. Rate of difference represents the ratio of difference of the rate of modal chromosome number between mcs (master cell stock) + n and mcs passages. The chromosomal analysis results showed that the ratio of difference of the rate of modal chromosome number between mcs + n and mcs passages was not more than 5%-15% and the structure aberrations was generally 0%-3%, not more than 5%-10%, thus the hereditary character of cell lines is comparatively stable without significant difference between different passages. The genetic characteristics of chromosomal number of cell lines determines their tumorigenicity, but it is species specific. Experimental models were established for the researches on the prevention and prophylaxis of malignant tumors or cancers and their genetically biological characteristics. Tests showed that there was correlation among cell line chromosome number variations, anchorage independence in soft agar, agglutination under plant lectins and tumor-forming ability in nude mice. Since testing in vitro is more economic, simpler, faster, and is thought to be reliable, we recommend plant lectins followed by SA or analysis of karyotypes as the initial means for monitoring tumorigenicity of animal cell line in nude mice.

BRCA1 is differentially expressed in human tumor cells

Mutations of the human breast cancer susceptibility gene 1 (BRCA1) confers a risk for breast, ovarian and prostate cancers and BRCA1 exerts multiple biological functions. Using Western blot and semi-quantitative reverse transcription-polymerase chain reaction (RT-PCR) assays, we have determined the expression of endogenous BRCA1 protein and mRNA in forty-three human tumor cell lines established from eleven types of human tumor tissues. BRCA1 was differentially expressed in tumor cell lines. No significant association was found between BRCA1 expression and the p53 gene status of cell lines. The disruption of wild-type p53 by either the human papillomavirus E6 oncogene or the mutant p53 gene (143Ala-->Val) did not cause any significant alteration in basal level of BRCA1 expression, while the knockout of p21 (-/-) by homologous recombination assay and Blocking Gadd45 expression by constitutive antisense expression slightly increased BRCA1 protein expression. Therefore, although the functional significance of the differential expression in human tumor cells is currently unknown, the present data provide a valuable background for further study of BRCA1 in tumor cell lines.