HIV-1 gag与gp41基因片段的序列特征与亚型研究

本文对华北地区出入境39例HIV-1阳性样本(中国21例,非洲17例,东南亚1例)的gag和env两个基因片段进行了序列特征和亚型对比分析。发现了A、A1、A3、B、C、G亚型和重组亚型03_AB、01_AE、AG、02_AG、07_BC、08_BC、CD和06_CPX共14个亚型,其中重组亚型占57.2%(8/14)。表明HIV-1基因变异较快,亚型分布广泛,重组亚型有增多趋势。此外发现26.7%(8/30)的样本,其gag和env基因区亚型表现不一致。提示在研究HIV-1亚型中应综合gag和env两个基因区的序列特征进行亚型分析。     

Regulation of idiotope expression. IV. Genetic linkage of two D region-dependent T15 idiotopes to the IgH allotype

The idiotopic (Id) repertoire of antibody response to phosphocholine was studied in mouse strains with different IgH allotypes. The T15 idiotype-bearing (T15+) serum antibody and antibody plaque-forming cells (PFC) were characterized with four monoclonal anti-Id that recognize distinct Id determinants on T15+ antibody encoded by VH-1 (of the S107 gene family), DH FL16.1, JH-1 and Vk22 germ-line genes. We have previously shown that expression of the Id designated AB1-2 and B36-82 depends on the third hypervariable loop (D region), whereas the other Id, MaId5-4 and B24-44, are influenced by VH structures outside of the D region. All four Id were expressed in the PC-response of all mouse strains tested, except the Ighj strains (C3H/HeJ, CBA/H-T6, PL/j), where the D region-dependent Id, AB1-2 and B36-82, were absent. The other Id, however, were normally expressed on individual PFC as well as the serum antibody of the Ighj strains. Expression of AB1-2 and B36-82 on 50% of PFC occurred in (BALB/c-Igha x C3H/HeJ-Ighj)F1 mice. The absence of Id correlated with a unique RFLP of the S107 gene family in Ighj strains. Finally, Id expression segregated with the appropriate RFLP pattern in individual (BALB/c x C3H/HeJ)F2 mice. These data demonstrate a selective genetic linkage of discrete T15 Id determinants, AB1-2 and B36-82 with the Igh allotype. By comparing these results with the available Ig sequences, we suggest that the Ighj allotype may be associated with an allelic form of the DH-FL16.1 segment which with VH-1, JH-1, and the Vk 22 code for the phosphocholine-specific antibody in the mouse.     

Nucleotide sequencing analysis of the swine 433-kb genomic segment located between the non-classical and classical<Emphasis Type="Italic"> SLA</Emphasis> class I gene clusters

Genome analysis of the swine leukocyte antigen (SLA) region is needed to obtain information on the MHC genomic sequence similarities and differences between the swine and human, given the possible use of swine organs for xenotransplantation. Here, the genomic sequences of a 433-kb segment located between the non-classical and classical SLA class I gene clusters were determined and analyzed for gene organization and contents of repetitive sequences. The genomic organization and diversity of this swine non-class I gene region was compared with the orthologous region of the human leukocyte antigen (HLA) complex. The length of the fully sequenced SLA genomic segment was 433 kb compared with 595 kb in the corresponding HLA class I region. This 162-kb difference in size between the swine and human genomic segments can be explained by indel activity, and the greater variety and density of repetitive sequences within the human MHC. Twenty-one swine genes with strong sequence similarity to the corresponding human genes were identified, with the gene order from the centromere to telomere of HCR - SPR1 - SEEK1 - CDSN - STG - DPCR1 - KIAA1885 - TFIIH - DDR - IER3 - FLOT1 - TUBB - KIAA0170 - NRM - KIAA1949 - DDX16 - FLJ13158 - MRPS18B - FB19 - ABCFI - CAT56. The human SEEK1 and DPCR1 genes are pseudogenes in swine. We conclude that the swine non-class I gene region that we have sequenced is highly conserved and therefore homologous to the corresponding region located between the HLA-C and HLA-E genes in the human.The nucleotide sequence data reported in this paper have been submitted to DDBJ, EMBL and GenBank databases under accession numbers AB113354, AB113355, AB113356, AB113357     

CXCR2基因多态性与奶牛乳房炎和乳品质的关联

采用PCR-SSCP技术研究了荷斯坦牛、西门塔尔牛和通江黄牛3个品种共160头个体CXCR2基因多态性与乳房炎抗性性状和对牛奶品质性状的遗传效应。结果表明: CXCR2基因有3个SNP多态位点, 分别位于序列的第685 bp、777 bp和861 bp位点, 确定了5个等位基因A、B、C、E和F。685 bp位点表现为BC和CC基因型, 777 bp位点表现为AA和AB基因型, 861 bp位点为CC和BC基因型。与奶牛乳房炎敏感性有关的基因型主要是BC、CC和FF, 可能对乳房炎有抗性的是AA、AB和EE基因型。据不同基因型对乳品质的遗传效应分析来看, AA、AB和EE基因型的乳品质性状极显著或显著优于其他基因型。     

VH4 gene segments dominate the intrathecal humoral immune response in multiple sclerosis

A characteristic feature of the CNS inflammatory response in multiple sclerosis (MS) is the intrathecal synthesis of IgG and the presence of oligoclonal bands. A strong correlation between CD138(+) plasma blast numbers in MS cerebrospinal fluid (CeSF) and intrathecal IgG synthesis suggests that these cells are the major Ab-secreting cell type in MS CeSF. Sequencing of V regions from CD138(+) cells in MS CeSF has revealed somatically mutated and expanded IgG clonotypes consistent with an Ag-targeted response. In the present study, single-cell RT-PCR analysis of CD138(+) cells from 11 MS patients representing differing clinical courses and stages of disease identified expansion of CD138(+) cells with functionally rearranged V(H)4 gene segments as an overriding feature of MS CeSF repertoires. V(H)4 dominance was attributed to the preferential selection of specific V(H)4 genes, particularly gene segment V(H)4-39, which displayed a significant enrichment in CeSF compared with MS peripheral blood B cells. A modest increase in V(H)4 prevalence among MS peripheral blood IgG memory cells was also noted, suggesting that factors shaping the CD138 repertoire in CeSF might also influence the peripheral IgG memory cell pool. These results indicate a highly restricted B cell response in MS. Identifying the targets of CeSF plasma cells may yield insights into disease pathogenesis.     

山羊GOLA-DQA2基因多态性与血液免疫性状的相关分析

文章采用PCR-RFLP技术对莱芜黑山羊、波尔山羊、鲁波山羊3个山羊种群的GOLA-DQA2基因外显子2进行遗传多态性研究, 并对其血液免疫指标的效应进行分析。结果表明, 3个山羊种群共检测到4种基因型, 由3个等位基因控制; GOLA-DQA2基因外显子2的第77、79、80和169位的碱基表现出多态性; 多数血液免疫指标品种效应是主要效应; 鲁波山羊中, AB基因型的红细胞计数、白细胞计数分别显著高于BB基因型、BC基因型(P<0.05); AB基因型的红细胞压积显著高于BB、BC 基因型(P<0.05); BC基因型的噬中性粒细胞比率显著高于BB基因型(P<0.05); 波尔山羊和莱芜黑山羊中, 基因型与血液免疫指标之间也有一定的相关性, 但没有达到显著水平。由上述结果初步推测, 在鲁波山羊中, AB、BC基因型是影响红细胞计数、白细胞总数、噬中性粒细胞比率等血液免疫指标的重要因素。研究结果揭示GOLA-DQA2基因与血液免疫指标之间有一定的相关性, 可为山羊的抗病育种提供一定的参考。     

含有抗白粉病基因的黑麦染色体小片段向小麦的转移

利用感白粉病的小麦品种绵阳11的纯系和黑麦自交系R12杂交, 在其单体附加系自交后代的BC₁F₅株系中选择小麦－黑麦异源易位系。根据已报道的黑麦特异重复序列pSc20H设计了一对特异引物, 用PCR方法鉴定了300个单体附加系的自交BC₁F₅株系,发现其中70个株系含有黑麦染色体成分。一个来源于6R单体附加系的小麦株系96Ⅱ691-830-98表现了对白粉病的高度抗性, PCR方法鉴定证明其含有黑麦染色体成分。对该株系作进一步的基因组原位杂交(GISH)鉴定, 证明它的一对染色体的端部含有黑麦染色体的小片段。这一结果指出, 含有抗白粉病基因的黑麦染色体6R小片段被引入了小麦。研究表明利用单体附加诱导染色体小片段易位是一种有效的方法。利用PCR和GISH原位杂交相结合的方法可提高检测外源染色体小片段的准确性和选择效率。     

The D-JH complex is an intermediate to the complete immunoglobulin heavy-chain V-region gene

We have examined the organization of the immunoglobulin JH segments in three clones derived from a single Abelson murine leukemia virus-transformed cell. Cloning and nucleotide sequence analyses of the JH-containing fragments have revealed the rearrangement from the preformed D-JH complex to the complete VH-D-JH gene, which was accompanied by the expression of the intra-cytoplasmic mu chain. In one case a JH segment downstream to the preformed D-JH was used to create a new VH-D-JH gene. Upon the D-JH and VH-D-JH rearrangements the intervening D segments were deleted from the chromosome. One of the expressed VH genes suffered from a large deletion of the 3' portion (including the 95th cysteine residue) of the VH segment. We discuss the possible mechanism of the allelic exclusion.     

Genomic sequence analysis of the 238-kb swine segment with a cluster of TRIM and olfactory receptor genes located, but with no class I genes, at the distal end of the SLA class I region

Continuous genomic sequence has been previously determined for the swine leukocyte antigen (SLA) class I region from the TNF gene cluster at the border between the major histocompatibility complex (MHC) class III and class I regions to the UBD gene at the telomeric end of the classical class I gene cluster (SLA-1 to SLA-5, SLA-9, SLA-11). To complete the genomic sequence of the entire SLA class I genomic region, we have analyzed the genomic sequences of two BAC clones carrying a continuous 237,633-bp-long segment spanning from the TRIM15 gene to the UBD gene located on the telomeric side of the classical SLA class I gene cluster. Fifteen non-class I genes, including the zinc finger and the tripartite motif (TRIM) ring-finger-related family genes and olfactory receptor genes, were identified in the 238-kilobase (kb) segment, and their location in the segment was similar to their apparent human homologs. In contrast, a human segment (alpha block) spanning about 375 kb from the gene ETF1P1 and from the HLA-J to HLA-F genes was absent from the 238-kb swine segment. We conclude that the gene organization of the MHC non-class I genes located in the telomeric side of the classical SLA class I gene cluster is remarkably similar between the swine and the human segments, although the swine lacks a 375-kb segment corresponding to the human alpha block. The nucleotide sequence data reported in this paper have been submitted to DDBJ, EMBL, and GenBank databases under accession numbers AB158486 and AB158487     

Etiology of MNU-induced melanomas in Xiphophorus hybrids

Genetic hybrids of the genus Xiphophorus have historically been useful models for study of the genetic aspects of tumor formation. In the most studied Xiphophorus tumor model, two-gene loci, XMRK and DIFF, are implicated as critical both to UV-induced and spontaneous melanoma formation in BC(1) hybrids of crosses between X. maculatus and X. helleri, with X. helleri as the recurrent backcross parent. In addition to UV, the direct-acting carcinogen N-methyl-N-nitrosourea (MNU) has been used to induce tumors in Xiphophorus BC(1) hybrids from several cross types. In the present study, we address the hypothesis that excess melanomas in MNU-treated BC(1) hybrids may have been generated by direct mutation of CDKN2AB, a candidate gene for DIFF. MNU treatment of F(1) and BC(1) hybrid fish significantly increased tumor incidence at 6 months; however, no association was found between MNU-induced tumor formation and zygosity of the candidate tumor tumor-suppressor CDKN2AB in BC(1) hybrids, consistent with previously reported results. Sequence analysis of the X. maculatus CDKN2AB locus of heterozygous individuals (both BC(1) and F(1) hybrids) did not reveal any mutations caused by MNU, suggesting that the mechanism of MNU-induced melanoma formation in this Xiphophorus model does not involve direct mutation of CDKN2AB but may result from mutation of other critical genes.     

抗动物病原菌芽孢杆菌的筛选、初步鉴定和抗菌活性

从鸡肠道分离、挑选的18株芽孢杆菌经培养特征、形态观察、生理生化实验,初步被鉴定为枯草芽孢杆菌(Bacillus subtilus)、地衣芽孢杆菌(Bacillus licheniformis)、蜡状芽孢杆菌(Bacillus cereus)、巨大芽孢杆菌(Bacillus megaterium)和凝结芽孢杆菌(Bacillus coagulans)。同时测定了它们对5种常见动物病原菌大肠杆菌(E.coli)、金黄色葡萄球菌(Staphylococcus aureus)、肠炎沙门氏菌(Salmonella typhimurium)、猪链球菌(Streptococcus suis)、奇异变形杆菌(Proteus mirabilis)的抑菌活性,其中有4株芽孢杆菌对5种病原菌都有抑制作用。还分别测定了它们产木聚糖酶(从0.895 U1到3.239 U1)和纤维素酶活性(分别为0.391 U2和0.465 U2)。结果表明,芽孢杆菌分离株BC17、BC32、BC106、BC228、BC247和BC261具有作为益生菌的开发潜力。     

Determination of local conformational stability in fragment 96-133 of bovine growth hormone by high-resolution H NMR spectroscopy

The specific assignment of resonances in the 400-MHz nuclear magnetic resonance (NMR) spectrum of fragment 96-133 (AII) of bovine growth hormone (bSt) is described. Assignments have been made with homonuclear two-dimensional techniques, in particular that of sequential resonance assignment. Complete assignments were possible for the spin systems of 16 residues out of a total of 38 and partial assignments for another 5. Assignment of resonances to either residue type or a class of residue was possible for a number of other spin systems. Analysis of the type of nuclear Overhauser effect (NOE) indicates that segments 96-110 and 130-133 are nonregular stable structures and that the segment 111-127, which putatively spans the alpha-helix, is not sufficiently stable to generate NOEs.     

Induction and transmission of wheat-Haynaldia villosa chromosomal translocations

In order to develop more wheat-Haynaldia villosa translocations involving different chromosomes and chromosome segments of H. villosa, T. durum-H, villosa amphiploid was irradiated with ^60Co γ-rays at doses of 800, 1,200, and 1,600 rad. Pollen collected from the spikes 1, 2, and 3 days after irradiation were transferred to emasculated spikes of the common wheat cv. ‘Chinese Spring＇. Genomic in situ hybridization was used to identify wheat-H, villosa chromosome translocations in the M1 generation. Transmission of the identified translocation chromosomes was analyzed in the BC1, BC2, and BC3 generations. The results indicated that all three irradiation doses were highly efficient for inducing wheat-alien translocations without affecting the viability of the M1 seeds. Within the range of 800-1,600 rad, both the efficiency of translocation induction and the frequency of interstitial chromosome breakage-fusion increased as the irradiation dosage increased. A higher translocation induction frequency was observed using pollen collected from the spikes 1 day after irradiation over that of 2 or 3 days after irradiation. More than 70% of the translocations detected in the M1 generation were transmitted to the BC1 through the female gametes. All translocations recovered in the BC1 generation were recovered in the following BC2, and BC3 generations. The transmission ability of different translocation types in different genetic backgrounds showed an order of ‘whole-arm translocation 〉 small alien segment translocation 〉 large alien segment translocation＇, through either male or female gametes, In general, the transmission ability through the female gametes was higher than that through the male gametes. By this approach, 14 translocation lines that involved different H. villosa chromosomes have been identified in the BC3 using EST-STS markers, and eight of them were homozygous.     

Transmembrane segment (TMS) VIII of the Na(+)/Citrate transporter CitS requires downstream TMS IX for insertion in the Escherichia coli membrane.

The amino acid sequence of the sodium ion-dependent citrate transporter CitS of K. pneumoniae contains 12 hydrophobic stretches that could form membrane-spanning segments. A previous analysis of the membrane topology in Escherichia coli using the PhoA gene fusion technique indicated that only nine of these hydrophobic segments span the membrane, while three segments, Vb, VIII and IX, were predicted to have a periplasmic location (Van Geest, M., and Lolkema, J. S. (1996) J. Biol. Chem. 271, 25582-25589). A topology study of C-terminally truncated CitS molecules in dog pancreas microsomes revealed that the protein traverses the endoplasmic reticulum membrane 11 times. In agreement with the PhoA fusion data, segment Vb was predicted to have a periplasmic location, but, in contrast, segments VIII and IX were found to be membrane-spanning (Van Geest, M., Nilsson, I., von Heijne, G., and Lolkema, J. S. (1999) J. Biol. Chem. 274, 2816-2823). In the present study, using site-directed Cys labeling, the topology of segments VIII and IX in the full-length CitS protein was determined in the E. coli membrane. Engineered cysteine residues in the loop between the two segments were accessible to a membrane-impermeable thiol reagent exclusively from the cytoplasmic side of the membrane, demonstrating that transmembrane segments (TMSs) VIII and IX are both membrane-spanning. It follows that the folding of CitS in the E. coli and endoplasmic reticulum membrane is the same. Cysteine accessibility studies of CitS-PhoA fusion molecules demonstrated that in the E. coli membrane segment VIII is exported to the periplasm in the absence of the C-terminal CitS sequences, thus explaining why the PhoA fusions do not correctly predict the topology. An engineered cysteine residue downstream of TMS VIII moved from a periplasmic to a cytoplasmic location when the fusion protein containing TMSs I-VIII was extended with segment IX. Thus, downstream segment IX is both essential and sufficient for the insertion of segment VIII of CitS in the E. coli membrane.     

Regulation of idiotope expression. III. H-2 influences the magnitude and the idiotypy of a T-independent antibody response in mice of certain genetic backgrounds

Antibody response to the phosphocholine (PC) epitope on Streptococcus pneumoniae R36a (Pn), a T-independent Ag type 2, was studied in H-2 congenic mouse strains. The PC-specific antibody plaque-forming cells (PFC) were enumerated in the spleen at various intervals after the primary Pn injection, and the proportion of PFC that produced antibody expressing the AB1-2 idiotope (Id) was determined by using the corresponding monoclonal anti-Id. AB1-2 is a cross-reactive Id, detectable on germline-encoded PC antibody of the T15 family, and on most, but not all, somatic variants of that antibody. The specific PFC responses in BALB/c (H-2d) and BALB.B (H-2b) strains were of comparable magnitude and most, if not all, PFC were ABl-1 Id-positive (AB1-2+). This was not the case in the responses of the B10D2 (H-2d) vs C57BL/10 (H-2b) strains and the D1.C (H-2d) vs D1.LP (H-2b) strains (on DBA/1 background). In each of these pairs, the H-2d mice were high responders, and the response was dominated by AB1-2 Id (greater than or equal to 80% AB1-2+ PFC at the peak, on day 5). The H-2b mice were low responders, and only a minor proportion of PFC (less than or equal to 30%) were AB1-2+; an increase of AB1-2+ was seen later in the response (d.10). The results of PFC assays were confirmed by measuring the PC-binding antibody and AB1-2 Id in the sera of D1.C and D1.LP mice immunized repeatedly with Pn. Moreover, D1.LP mice that had very low levels of AB1-2 Id had higher serum levels of antibody expressing two other T15 Id, B36-82, and B24-44. The B36-82 and B24-44 Id have been previously found on somatic variants of PC antibody expressed independently of the Ab1-2 Id. The concentrations of these two Id in D1.LP mice after repeated immunization approached those in D1.C. These results indicate that 1) the H-2 allelism may have a significant effect on TID antibody response in mice of a certain genetic background, but not in the BALB/c; and 2) the idiotypic repertoire of the response may be influenced by H-2 at the level of clonal variants of PC-reactive cells.     

Structural insights into parallel strategies for germline antibody recognition of lipopolysaccharide from Chlamydia

The structure of the antigen-binding fragment from the monoclonal antibody S64-4 in complex with a pentasaccharide bisphosphate fragment from chlamydial lipopolysaccharide has been determined by x-ray diffraction to 2.6 ? resolution. Like the well-characterized antibody S25-2, S64-4 displays a pocket formed by the residues of germline sequence corresponding to the heavy and light chain V gene segments that binds the terminal Kdo residue of the antigen; however, although S64-4 shares the same heavy chain V gene segment as S25-2, it has a different light chain V gene segment. The new light chain V gene segment codes for a combining site that displays greater affinity, different specificity, and allows a novel antigen conformation that brings a greater number of antigen residues into the combining site than possible in S25-2. Further, while antibodies in the S25-2 family use complementarity determining region (CDR) H3 to discriminate among antigens, S64-4 achieves its specificity via the new light chain V gene segment and resulting change in antigen conformation. These structures reveal an intriguing parallel strategy where two different combinations of germline-coded V gene segments can act as starting points for the generation of germline antibodies against chlamydial antigens and show how anti-carbohydrate antibodies can exploit the conformational flexibility of this class of antigens to achieve high affinity and specificity independently of CDR H3.     

Salinity tolerance of Cornus sericea seedlings from three provenances

Red-osier dogwood (Cornus sericea L.) seedlings from three seed sources of different climatic conditions were treated hydroponically with 0?C100?mM NaCl to compare their salinity tolerance. The control seedlings from the coldest location, Alberta (AB) had the lowest biomass and transpiration rate, as well as the highest photosynthetic water use efficiency. When exposed to 100?mM NaCl for 1?week, the seedlings from AB maintained a higher photosynthetic rate and stomatal conductance than the seedlings from the low precipitation location, British Columbia (BC), and the high precipitation location, New Brunswick (NB). After 2?weeks of treatment at this highest salt concentration, leaf injury occurred in the plants from all the locations suggesting that in spite of early differences, the seedlings from all locations may not be able to survive the salinity stress over time. In contrast, when plants were exposed to 50?mM NaCl, the seedlings from AB had low level of leaf injury, followed by the plants from BC compared with the NB seedlings. Furthermore, at this moderate salt concentration, the seedlings from NB (with the highest biomass for the control) had the lowest root relative growth rate and the highest leaf area; while the seedlings from AB and BC had the highest photosynthetic water use efficiency. The seedlings from AB were able to retain more K in the roots than the seedlings from NB, suggesting a higher level of salinity tolerance. Lower chloride content was observed in the leaves of the AB seedlings than in the BC seedlings. The results of this study show that when exposed to 50?mM NaCl, the seedlings from the cold (AB) and dry (BC) locations had higher salt tolerance than the seedlings from the milder climate (NB). These results suggest that cross tolerance may occur in red-osier dogwood; however, it varies depending on the level of salinity stress.     

Immunoglobulin gene rearrangements in normal mouse B cells.

We have analyzed the structure of rearranged mu heavy-chain genes obtained from the genomic DNA of normal BALB/c mouse spleen cells expressing surface immunoglobulin M. Examples were found of two types of nonproductive rearrangements, which may be responsible for allelic exclusion in normal B cells. In one of these rearrangements, a germ line D gene segment has joined to the JH4 gene segment but no V/D joining has occurred. We present evidence that D gene segments lie as a cluster between V and J gene segments in the germ line. A comparison of conserved sequences in V and D gene segments suggests that the D gene segments, which are found only in the heavy-chain gene family, may have evolved from V gene segments similar to the Vk family.     

Genetic analysis of the cell binding domain region of the chicken fibronectin gene

We have determined the nucleotide sequence of the cell binding domain region of the chicken fibronectin gene and analyzed it evolutionaly. We present here the complete nucleotide sequence of 4.3 kb HindIII/EcoRI segment from the clone lambda FC23 of the chicken fibronectin gene. There were five exons in this segment. When we lined up the amino acid of exons 28, 29 and 31, three alignments, known as the Type III repeat, appeared. Tetrapeptide, -RGDS-, called the cell binding domain, existed in the second repeat, coding exon 30. It was presumed that the Type III repeats were composed of two exons in the chicken gene, the same as in the rat and humans. We found repeatedly appearing amino-acid sequences such as -TIT- (three arrays in these Type III repeats) but also found one of the amino acids substituted in the tripeptide in these Type III repeats (seven arrays). We analyzed these repeats from the point of view of evolution. We used three of the nucleotide sequences (12-18 bp) coding such -TIT- repeats as a unit length for comparing the various homologies after dividing the coding region into 56 segments. The mutual homology of the divided segments to each one of three showed 53% on average. On the other hand, the mutual nucleotide homology of the Type III repeat was 44%. This suggested that the Type III repeat may have been developed by frequent duplication of small gene units.