Genetic and pathogenic characterization of new infectious bronchitis virus strains in the GVI-1 and GI-19 lineages isolated in central China

Avian infectious bronchitis(IB)is a highly contagious infectious disease caused by infectious bronchitis virus(IBV),which is prevalent in many countries worldwide and causes serious harm to the poultry industry.At present,many commercial IBV vaccines have been used for the prevention and control of IB;however,IB outbreaks occur frequently.In this study,two new strains of IBV,SX/2106 and SX/2204,were isolated from two flocks which were immunized with IBV H120 vaccine in central China.Phylogenetic and recombination analysis indicated that SX/2106,which was clustered into the GI-19 lineage,may be derived from recombination events of the GI-19 and GI-7 strains and the LDT3-A vaccine.Genetic analysis showed that SX/2204 belongs to the GVI-1 lineage,which may have originated from the recombination of the GI-13 and GVI-1 strains and the H120 vaccine.The virus cross-neutralization test showed that the antigenicity of SX/2106 and SX/2204 was different from H120.Animal experiments found that both SX/2106 and SX/2204 could replicate effectively in the lungs and kidneys of chickens and cause disease and death,and H120 immunization could not provide effective protection against the two IBV isolates.It is noteworthy that the pathogenicity of SX/2204 has significantly increased compared to the GVI-1 strains isolated previously,with a mortality rate up to 60%.Considering the continuous mutation and recombination of the IBV genome to produce new variant strains,it is important to continuously monitor epidemic strains and develop new vaccines for the prevention and control of IBV epidemics.

Phylotranscriptomic discordance is best explained by incomplete lineage sorting within Allium subgenus Cyathophora and thus hemiplasy accounts for interspecific trait transition

The transition of traits between genetically related lineages is a fascinating topic that provides clues to understanding the drivers of speciation and diversification.Much can be learned about this process from phylogeny-based trait evolution.However,such inference is often plagued by genome-wide gene-tree discordance(GTD),mostly due to incomplete lineage sorting(ILS)and/or introgressive hybridization,especially when the genes underlying the traits appear discordant.Here,by collecting transcriptomes,whole chloroplast genomes(cpDNA),and population genetic datasets,we used the coalescent model to turn GTD into a source of information for ILS and employed hemiplasy to explain specific cases of apparent“phylogenetic discordance”between different morphological traits and probable species phylogeny in the Allium subg.Cyathophora.Both concatenation and coalescence methods consistently showed the same phylogenetic topology for species tree inference based on single-copy genes(SCGs),as supported by the KS distribution.However,GTD was high across the genomes of subg.Cyathophora:~27%e38.9%of the SCG trees were in conflict with the species tree.Plasmid and nuclear incongruence was also present.Our coalescent simulations indicated that such GTD was mainly a product of ILS.Our hemiplasy risk factor calculations supported that random fixation of ancient polymorphisms in different populations during successive speciation events along the subg.Cyathophora phylogeny may have caused the character transition,as well as the anomalous cpDNA tree.Our study exemplifies how phylogenetic noise can be transformed into evolutionary information for understanding character state transitions along species phylogenies.

Myeloid sarcoma as the only manifestation in a rare mixed lineage leukemia-fusion-driven acute myeloid leukemia:A case report

BACKGROUND The mixed lineage leukemia(MLL)-eleven-nineteen lysine-rich leukemia(ELL)fusion gene is a rare occurrence among the various MLL fusion genes.We present the first case in which myeloid sarcoma(MS)was the only manifestation of adult MLL-ELL-positive acute myeloid leukemia(AML).CASE SUMMARY We report a case of a 33-year-old male patient who was admitted in June 2022 with a right occipital area mass measuring approximately 7 cm×8 cm.Blood work was normal.The patient underwent right occipital giant subscalp mass excision and incisional flap grafting.Immunohistochemistry was positive for myeloperoxidase,CD43 and CD45 and negative for CD3,CD20,CD34,and CD56.The bone marrow aspirate showed hypercellularity with 20%myeloblasts.Flow cytometry showed that myeloblasts accounted for 27.21%of the nucleated cells,which expressed CD33,CD38,and CD117.The karyotype was 46,XY,t(11,19)(q23;p13.1),-12,+mar/46,XY.Next-generation sequencing showed a fusion of MLL exon 7 to exon 2 of ELL.A diagnosis of MLL-ELL-positive AML(M2 subtype)with subcutaneous MS was made.CONCLUSION MLL-ELL-positive AML with MS is a rare clinical entity.Additional research is needed to elucidate the molecular mechanisms of the pathogenesis of MS.

美国PRRSV 1-4-4 Lineage 1C新型变异株的基因组特征和传入我国的风险分析

猪繁殖与呼吸综合征(Porcine Reproductive and Respiratory Syndrome,PRRS)是严重危害生猪产业的疾病之一,呈全球性流行,其病原猪繁殖与呼吸综合征病毒(Porcine Reproductive and Respiratory Syndrome Virus,PRRSV)具有毒株多样、易变异重组且异源毒株交叉保护不足的特点。2020年10月以来,在美国中西部地区发现一种新型PRRSV 1-4-4 Lineage 1C变异株,其较以往美国流行毒株致病性更强,感染可引起成年母猪死亡,传播更迅速,且现有疫苗对其保护效果不佳。鉴于中美间有大量种猪和猪肉制品贸易,且美国PRRSV毒株曾多次传入我国,该变异株的流行情况、基因组特征、致病性、传入风险以及现有检测方法和防控技术对其有效性等均成为业界关注重点。本文对新型PRRSV 1-4-4 Lineage 1C变异株在美国暴发和流行的情况、分子特征及传入我国的风险进行了总结分析,旨在提高对新型变异株的认识,加强防控技术储备,以保障我国养猪业安全稳定发展。

Negative regulation of miRNA-9 on oligodendrocyte lineage gene 1 during hypoxic-ischemic brain damage

Oligodendrocyte lineage gene 1 plays a key role in hypoxic-ischemic brain damage and myelin repair, miRNA-9 is involved in the occurrence of many related neurological disorders. Bioin- formatics analysis demonstrated that miRNA-9 complementarily, but incompletely, bound oligodendrocyte lineage gene 1, but whether miRNA-9 regulates oligodendrocyte lineage gene 1 remains poorly understood. Whole brain slices of 3-day-old Sprague-Dawley rats were cultured and divided into four groups： control group; oxygen-glucose deprivation group （treatment with 8% O2 ＋ 92% N2 and sugar-free medium for 60 minutes）; transfection control group （after oxygen and glucose deprivation for 60 minutes, transfected with control plasmid） and miRNA-9 transfection group （after oxygen and glucose deprivation for 60 minutes, transfected with miRNA-9 plasmid）. From the third day of transfection, and with increasing culture days, oligodendrocyte lineage gene 1 expression increased in each group, peaked at 14 days, and then decreased at 21 days. Real-time quantitative PCR results, however, demonstrated that oligoden- drocyte lineage gene 1 expression was lower in the miRNA-9 transfection group than that in the transfection control group at 1, 3, 7, 14, 21 and 28 days after transfection. Results suggested that miRNA-9 possibly negatively regulated oligodendrocyte lineage gene 1 in brain tissues during hypoxic-ischemic brain damage.

Lineage tracing of direct astrocyte-to-neuron conversion in the mouse cortex

Regenerating functional new neurons in the adult mammalian central nervous system has been proven to be very challenging due to the inability of neurons to divide and repopulate themselves after neuronal loss.Glial cells,on the other hand,can divide and repopulate themselves under injury or diseased conditions.We have previously reported that ectopic expression of NeuroD1 in dividing glial cells can directly convert them into neurons.Here,using astrocytic lineage-tracing reporter mice(Aldh1l1-CreERT2 mice crossing with Ai14 mice),we demonstrate that lineage-traced astrocytes can be successfully converted into NeuNpositive neurons after expressing NeuroD1 through adeno-associated viruses.Retroviral expression of NeuroD1 further confirms that dividing glial cells can be converted into neurons.Importantly,we demonstrate that for in vivo cell conversion study,using a safe level of adeno-associated virus dosage(10^10–10^12 gc/mL,1μL)in the rodent brain is critical to avoid artifacts caused by toxic dosage,such as that used in a recent bioRxiv study(2×10^13 gc/mL,1μL,mouse cortex).For therapeutic purpose under injury or diseased conditions,or for non-human primate studies,adeno-associated virus dosage needs to be optimized through a series of dose-finding experiments.Moreover,for future in vivo gliato-neuron conversion studies,we recommend that the adeno-associated virus results are further verified with retroviruses that mainly express transgenes in dividing glial cells in order to draw solid conclusions.The study was approved by the Laboratory Animal Ethics Committee of Jinan University,China(approval No.IACUC-20180330-06)on March 30,2018.

Chromodomain-helicase-DNA binding protein 5, 7 and pronecrotic mixed lineage kinase domain-like protein serve as potential prognostic biomarkers in patients with resected pancreatic adenocarcinomas

Pancreatic cancer is one of the deadliest cancers with a very poor prognosis. Recently, there has been a significant increase in research directed towards identifying potential biomarkers that can be used to diagnose and provide prognostic information for pancreatic cancer. These markers can be used clinically to optimize and personalize therapy for individual patients. In this review, we focused on 3 biomarkers involved in the DNA damage response pathway and the necroptosis pathway: Chromodomainhelicase-DNA binding protein 5, chromodomain-helicaseDNA binding protein 7, and mixed lineage kinase domain-like protein. The aim of this article is to review present literature provided for these biomarkers and current studies in which their effectiveness as prognostic biomarkers are analyzed in order to determine their future use as biomarkers in clinical medicine. Based on the data presented, these biomarkers warrant further investigation,and should be validated in future studies.

Whole Genome Sequencing and Comparisons of Different Chinese Rabies Virus Lineages Including the First Complete Genome of an Arctic-like Strain in China

Objective To learn the rabies genome molecular characteristics and compare the difference of China rabies lineages. Methods The complete genomes of 12 strains from different China rabies lineages were amplified and sequenced, and all the China street strain genomes （total 43）, Arctic and Arctic-like genomes were aligned using ClustalX2, the genome homologies were analyzed using MegAlign software, and the phylogenetic trees were constructed by MEGA 5. Results First Arctic-like rabies genome in China （CO, H1202D） was reported, and we supplemented the rabies genome data of China, ensuring at least one genome was available in each China lineage. The genome size of China V （11908nt） is obviously shorter than other lineages＇ （11923-11925nt） for the difference of N-P non-coding regions. Among different lineages, the genome homologies are almost under 90%. CQH1202D （China IV lineage） has close relationship with strains from South Korea and they share about 95% genome similarities. Conclusion The molecular characteristics of 6 different China rabies lineages were compared and analyzed from genome level, which benefits for continued comprehensive rabies surveillance, rabies prevention and control in China.

The Epidemiological Characteristics of Beijing Lineage Mycobacterium tuberculosis from a National Referral Center in China

Our study was to investigate the epidemiological characteristics of M.tuberculosis from a national tuberculosis referral center in China. All strains isolated from TB patients, were genotyped by the RD105 deletion, 8 and 51 SNP loci and VNTR. The high differentiation SNPs of modern Beijing strains were analyzed for protein function and structure. 413 M. tuberculosis were included. Of 379 Beijing lineage M. tuberculosis, ＇modern＇ and ＇ancient＇ strains respectively represented 85.5% （324/379） and 14.5% （55/379）. Rv2494 （V48A） and Rv0245 （Sl03F） were confirmed as high differentiation SNPs associated with modern strains. In a word, Modern Beijing lineage M.tuberculosis was dominant and the structural models suggested that modern sub-lineage may more easily survive in ＇extreme＇ host condition.

DNA reveals long-distance partial migratory behavior in a cryptic owl lineage

Background: The Brown Hawk Owl complex is said to consist of three species,the Brown Boobook(Ninox scutulata),the Chocolate Boobook(Ninox randi) and the Northern Boobook(Ninox japonica),which includes the nominate migratory lineage Ninox japonica japonica and a mitochondrially distinct lineage of taxonomically uncertain status that has been recorded year-round at least in Taiwan.Overlap in ranges during migration and morphological similarity have led to difficulties in distinguishing the Brown Boobook from the Northern Boobook.Methods: PCR of cytochrome-b and Sanger sequencing of Ninox samples from Singapore and Brunei were used to determine sample identity.Results: Two out of four Singaporean samples and the Brunei sample were identified as Northern Boobooks.This is the first official record of this species in Singapore and represents a considerable range extension for the species.Further,the samples belong to the mitochondrially distinct lineage previously characterized in resident Taiwan Residents populations rather than to the well-known nominate migratory lineage.Conclusions: Our data show that the mitochondrial signature previously documented in resident Taiwan Residents populations of the Northern Boobook extends to migratory populations.This cryptic lineage may be more widespread in its breeding quarters,extending to the Chinese and Russian mainland,in which case the name florensis would apply to it.Further genetic and bioacoustic investigation is required to resolve the taxonomic status of this lineage.

Central nervous system and peripheral cell labeling by vascular endothelial cadherin-driven lineage tracing in adult mice

Understanding the contribution of endothelial cells to the progenitor pools of adult tissues has the potential to inform therapies for human disease.To address whether endothelial cells transdifferentiate into non-vascular cell types,we performed cell lineage tracing analysis using transgenic mice engineered to express a fluorescent marker following activation by tamoxifen in vascular endothelial cadherin promoter-expressing cells(VEcad-CreERT2;B6 Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze).Activation of target-cell labeling following 1.5 months of ad libitum feeding with tamoxifen-laden chow in 4–5 month-old mice resulted in the tracing of central nervous system and peripheral cells that include:cerebellar granule neurons,ependymal cells,skeletal myocytes,pancreatic beta cells,pancreatic acinar cells,tubular cells in the renal cortex,duodenal crypt cells,ileal crypt cells,and hair follicle stem cells.As Nestin expression has been reported in a subset of endothelial cells,Nes-CreERT2 mice were also utilized in these conditions.The tracing of cells in adult Nes-CreERT2 mice revealed the labeling of canonical progeny cell types such as hippocampal and olfactory granule neurons as well as ependymal cells.Interestingly,Nestin tracing also labeled skeletal myocytes,ileal crypt cells,and sparsely marked cerebellar granule neurons.Our findings provide support for endothelial cells as active contributors to adult tissue progenitor pools.This information could be of particular significance for the intravenous delivery of therapeutics to downstream endothelial-derived cellular targets.The animal experiments were approved by the Boise State University Institute Animal Care and Use Committee(approval No.006-AC15-018)on October 31,2018.

ATP binding cassette C1 (ABCC1/MRP1)-mediated drug efflux contributes to disease progression in T-lineage acute lymphoblastic leukemia

Purpose: In acute lymphoblastic leukemia (ALL), multidrug resistance is often mediated by AT- Pase Binding Cassette (ABC) proteins, which principally involve ABCC1 (multidrug resistance protein 1, MRP1) and ABCB1 (multidrug resistance 1, MDR1). However, direct comparisons between the differential effects of ABCC1 and ABCB1 have been difficult, since identical cell lines with differential expression of these transporters have not been developed. Experimental Design: In this study, we developed and compared the biological profiles of Jurkat cell lines that selectively over-expressed ABCC1 and ABCB1. Vincristine (VCR) plays an important role in the treatment of T-lineage ALL (T-ALL), and is often the first drug given to newly-diagnosed patients. Because of its importance in treatment, we provide descalating, sub-lethal doses of VCR to Jurkat cells, and extended our observations to expression profiling of newly diagnosed patients with T-ALL. Results: We found that VCR-resistant cells over-expressed ABCC1 nearly 30-fold. The calcein AM assay confirmed that VCR-resistant cells actively extruded VCR, and that ABCC1-mediated drug resistance conferred a different spectrum of multidrug resistance than other T-ALL induction agents. siRNA experiments that blocked ABCC1 export confirmed that VCR resistance could be reversed in vitro. Analyses of T-lymphoblasts obtained from 100 newly diagnosed T-ALL patients treated on Children’s Oncology Group Phase III studies 9404 and AALL0434 that induction failure could be could be partially explained by the over-expression of ABCC1 and ABCB1. Conclusions: Taken together, these results suggest that over-expression of ABC transporters plays a contributing role in mediating treatment failure in T-ALL, and underscore the need to employ alternate treatment approaches in patients for whom induction failed or for those with relapsed disease.

The Li Lineage of Traditional Chinese Medicine

Professor Li Ding(李鼎)is the founder and tenured professor,doctoral supervisor at Shanghai University of Traditional Chinese Medicine,a Representative Inheritor for China Intangible Cultural Heritage-Acupuncture and Moxibustion.It is well known that Chinese medicine is rooted in Chinese culture and history.The inheritance of Chinese medicine cannot be separated from the inheritance of Chinese culture and history.Professor Li Ding’s path of Chinese medicine inheritance perfectly reflects the above-mentioned laws and is worthy of further exploration and research.The full text of this article is divided into three parts and will be published one after another.The first part“The Lineage of Gu Yi Tang”brings us Li’s family historical stories;the second part“The Lineage of Chinese Studies”introduces professor Li’s Chinese culture studies;and the third part“The Lineage of Dao Sheng Tang”discusses professor Li's inheritance of Chinese medicine.This article will bring our readers a rich and colorful Chinese scroll painting,which not only focuses on Chinese Medicine,acupuncture but also touches ancient Chinese history culture,Daoism,and even more.

Immunological Responses against Different Lineages of Influenza B Antigen in School Children during Two Consecutive Seasons

While Influenza B viruses currently circulating worldwide are of two distinct evolutionary hemagglutinin lineages, current trivalent inactivated influenza virus vaccines (TIV) contain only a single component. Single doses of TIV containing B antigen of B/Florida/4/2006 (Yamagata-like) or B/Brisbane/60/2008 (Victoria-like) were administered during 2008/2009 and 2009/2010 influenza seasons, respectively. The objective of this study was to evaluate the immunological response against different lineages of B antigens in school-aged children. A non-randomized sero-epidemiological study was conducted and the immunogenicity responses based on sero-protection rate and geometric mean titre ratio (GMTR) of hemagglutination inhibition (HI) antibodies were measured before and after immunization as well as post-influenza season. Our results suggested that school-aged children under the age of 9 years receiving TIV vaccination induced and retained higher level of sero-protection rate (66.7% and 69% for the 2008-09 and 2009-10 season, respectively) to the homologous lineage than the heterologous lineage post-vaccination (19.4% and 27.6% for the 2008-09 and 2009-10 season, respectively). The need for the quadrivalent TIV by including both lineages of influenza B viruses is recommended in this study, particularly for children under the age of 9 years.

Building tissue niches for stem cell lineage specification

Introduction The success in lineage-specific differentiation of human embryonic and induced pluripotent stem(hES/iPS)cells raises new hopes for cell-based therapies.It is envisioned that cells differentiated from hES/iPS cells can be used to replace or repair damaged or diseased cells and tissues in body.This has not yet been possible due to the difficulty in generating biologically functional cells in vitro.While many factors may contribute to these failures,the lack of tissue niches in the current differentiation systems has been viewed in impairing the maturation of these cells.As revealed by studying mice embryo development,organ development requires strict temporal and spatial control at each stage.The stepwise hESC differentiation

Surrogate Role of CD85k on Monocytic Lineage Involved Leukemogenesis Biology and Clinical Aspect

Background: Unique receptor involved in leukemogenesis is CD85k;an immuneglobulin receptor for immune tolerance, CD36 is glycoprotein mediates cellular adhesion and metastatic spread, CD14, CD15 considered common monocytic markers. Aims: to investigate CD85k with monocytic lineage involved leukemia (MLIL) markers in leukemia pathogenesis and clinical presentation. Patients and Methods: 47 patients (32 diagnosed acute myeloid leukemia (AML);15 non-malignant hematological disease as a control), were included, aged from 2 to 80 years, all subjected to peripheral blood (P.Bl) and bone marrow (B.M) examination, immunophenotyping (IPT) using FASC Canto four color flow cytometer (FCM) Becton Dickenson (BD) USA, for CD13, CD33, MPO, HLA-DR, CD34, CD38, CD117, CD14, CD15 and CD36 the Mo Abs supplied by B.D Bioscience, and anti CD85k Mo Abs by Aveda de Coimbra Flamenco, reference No. 1399990130. Results: Frequency of CD85k is 19/32 (59.37%) of AML;14/14 (M4/M5) 100% positive CD85k, insignificant correlations of CD85k to sex, lymphadenopathy or organomegaly, platelets count and P.Bl blast (P > 0.05), significant to age 50,000 × 109/l, Hb 0.05). Conclusion: Although CD85k is MLIL associated marker, it is not correlated with other MLIL markers with frequency 100% in MLIL and 59.37% in AML, age predisposition is <35 years with no sex variation, significant correlation to progenitor and myeloid markers, it’s a crucial role in leukemogenesis biology, not in clinical presentations, considered good follow up predictor MLIL marker.

Expression of hypoxia-inducible factor 1 alpha and oligodendrocyte lineage gene-1 in cultured brain slices after oxygen-glucose deprivation

Oligodendrocyte lineage gene-1 expressed in oligodendrocytes may trigger the repair of neuronal myelin impairment, and play a crucial role in myelin repair. Hypoxia-inducible factor la, a transcription factor, is of great significance in premature infants with hypoxic-ischemic brain damage There is little evidence of direct regulatory effects of hypoxia-inducible factor le on oligodendrocyte lineage gene-l. In this study, brain slices of Sprague-Dawley rats were cultured and subjected to oxygen-glucose deprivation. Then, slices were transfected with hypoxia-inducible factor la or oligodendrocyte lineage gene-1. The expression levels of hypoxia-inducible factor la and oligodendrocyte lineage gene-1 were significantly up-regulated in rat brains prior to transfection, as detected by immunohistochemical staining. Eight hours after transfection of slices with hypoxia-inducible factor la, oligodendrocyte lineage gene-1 expression was upregulated, and reached a peak 24 hours after transfection. Oligodendrocyte lineage gene-1 transfection induced no significant differences in hypoxia-inducible factor la levels in rat brain tissues with oxygen-glucose deprivation. These experimental findings indicate that hypoxia-inducible factor la can regulate oligodendrocyte lineage gene-1 expression in hypoxic brain tissue, thus repairing the neural impairment.

Tumor cells undergoing direct lineage conversion to neurons: unnatural but useful?

Dear Editor, In 2011, Son et al. （2011） reported that the forced expression of selected transcription factors is sufficient to convert mouse and human fibroblasts into induced motor neurons （iMNs）. The authors used three factors （Ascll, Brn2, and Mytll） to convert fibroblasts into neuronal-like ceils. After confirming that the cells had neuronal morphology, but with absence of motor neuron markers, eight candidate transcription factors were added, which participate in various stages of motor neuron specification. As expected, a significant number of motor cells emerged with known characteristics of cultured embryonic motor neurons.

Identification of a novel mtDNA lineage B3 in chicken (Gallus gallus domesticus)

DEAR EDITOR, In this study, we sequenced the complete mitochondrial DNA genome （mitogenome） of the Zhengyang Yellow chicken （Gallus gallus domesticus） by next-generation sequencing technology. Samples were taken from Zhumadian city, Henan Province, China. The complete mitogenome was 16 785 bp in size, and had a nucleotide composition of 30.3% （A）, 23.7% （T） 32.5% （C）, and 13.5% （G）, with a high AT content of 54.0%. The assembled mitogenome exhibited typical mitochondrial DNA （mtDNA） structure, including a non-coding control region, two rRNA genes, 13 protein-coding genes, and 22 tRNA genes. Phylogenetic analysis indicated that this mitogenome defined a novel sub-haplogroup B3 within haplogroup B. These results should provide essential information for chicken domestication and insiqht into the evolution of genomes.

The Li Lineage of Traditional Chinese Medicine

Chinese medicine cannot be separated from Chinese culture and history.Professor Li Ding's path floridly embodies that,and so is worthy not just of admiration,but also of studious exploration.Aside from still,after well over half a century there,serving as a doctoral supervisor professor at the Shanghai University of Traditional Chinese Medicine(SHUTCM),and being one of the university's founders,he continues to contribute long after having been formally declared“A representative inheritor for China intangible cultural heritage-Acupuncture and Moxibustion.”This is the second article in a three-part series on Professo r.Li Ding.The first part focuses on“The Lineage of Gu Yi Tang,”and that storied our family history we will continue discussing now,with this second installment:"The Lineage of Chinese Studies,"which introduces professor Li's Chinese cultural studies.The forthcoming third part:“The Lineage of Dao Sheng Tang”will discuss professor Li's inheritance of Chinese medicine specifically.These three articles will bring our readers a rich and colorful Chinese scroll painting,which not only focus on acupuncture and general Chinese medicine,but also touch ancient Chinese history,culture,Taoism,and even more.