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Biomedical subjects

Y Hu

Publications and source records attributed to Y Hu.

At least 37 records · Page 2Linked to original sources
PubMed2005

Effect of segmental artery ligation on the blood supply of the thoracic spinal cord during anterior spinal surgery: a quantitative histomorphological fresh cadaver study.

STUDY DESIGN: Human cadaver quantitative morphometric analysis of the blood vessels in the spinal cord after ligation of segmental arteries. OBJECTIVES: To investigate the effect of ligation of segmental arteries on the quantity and density of the blood vessels in the spinal cord. SUMMARY OF BACKGROUND DATA: Ligation of segmental arteries is often used in the anterior approach for correction scoliosis. However, whether or not segmental artery ligation is liable to deny the spinal cord an adequate blood supply, thus leading to paraplegia, still remains controversial. METHODS: Eleven fresh cadavers were divided into control, unilateral, and bilateral groups. For the unilateral and bilateral groups, 5 segmental vertebral arteries (T7-T11) were ligated unilaterally and bilaterally, respectively. Then, the number and density of blood vessels at different levels in the 3 groups were measured. RESULTS: Compared to that of the corresponding level in the control group, the number of blood vessels at T5 to L1 all decreased in the ligation groups. And significant differences were found at T8 (82.80 +/- 16.36), T10 (77.80 +/- 19.80), and T11 (99.20 +/- 14.85) levels, compared to those of the corresponding levels in the control group: T8 (175.80 +/- 8. 31), T9 (176.40 +/- 32. 33), T10 (171.40 +/- 9. 73), and T11 (189.20 +/- 15. 92). Further decrease was found at each corresponding level in the bilateral group, and significant differences were found at T8 (65.80 +/- 15.55), T9 (24.80 +/- 13.43), T10 (0), T11 (0), and T12 (0) levels. Similar results were obtained with regard to the density of blood vessels. Significant differences were found at T11 (1.246 +/- 0.112) and L1 (1.349 +/- 0.109) in the unilateral group, and T9 (0.260 +/- 0.088), T10 (0), T11 (0), T12 (0), and L1 (0.147 +/- 0.117) in the bilateral group compared to those of the corresponding levels in the control group: T9 (1.810 +/- 0.202), T10 (1.833 +/- 0.175), T11 (2.308 +/- 0.335), T12 (2.510 +/- 0.617), and L1 (2.193 +/- 0.033). CONCLUSIONS: This study suggests that the more levels the ligation encompasses, the higher the risk of spinal cord damage. Therefore, caution should be taken when several segmental arteries are to be ligated in the clinical setting. What is more, bilateral ligation, which is worse than unilateral ligation, can lead to a significant decrease in the number and density of blood vessels of the spinal.

Adolescent↗
PubMed2005

The effect of isoforms of the cell polarity protein, human ASIP, on the cell cycle and Fas/FasL-mediated apoptosis in human hepatoma cells.

Human ASIP (hASIP) is expressed as numerous alternative splicing isoforms and there is an atypical protein kinease C (aPKC) phosphorylation site in exon 17b of the encoded sequence. We have identified an important role for exon 17b in cancer cells. Our results showed that hASIP-sa and sb had different effects on cell growth and Fas/FasL-mediated apoptosis in BEL-7404 human hepatoma cells. Human ASIP-sa modified the S phase of the cell cycle and might stimulate cell proliferation. Growth inhibition by hASIP-a antisense oligonucleotide-confirmed the positive action of hASIP-sa. Compared with hASIP-sa, hASIP-sb accelerated Fas/FasL-induced apoptosis, examined by sub-G1 accumulation, chromatin condensation, nuclear fragmentation, PARP cleavage, caspase-8 degradation and mitochondria- regulated cell death. Treatment with aPKC inhibitor could enhance Fas/FasL-mediated apoptosis in hASIP-sa-overexpressing cells, suggesting that hASIP-sa and its interaction with aPKC might contribute to the malignant growth and the blocking of Fas/FasL-mediated apoptosis, while hASIP-sb might function as an antagonist of hASIP-sa.

Agouti Signaling Protein↗
PubMed2005

Sequestration of As by iron plaque on the roots of three rice (Oryza sativa L.) cultivars in a low-P soil with or without P fertilizer.

A pot experiment was carried out in a greenhouse to investigate the sequestration of As in iron plaques on root surface of three rice (Oryza sativa L.) cultivars. Phosphate (P) fertilization increased both plant biomass and tissue P concentrations significantly, indicating that the soils used in this study was highly P-deficient. Results from this study confirmed that low P supply improved the formation of iron plaque on rice roots. As a consequence, arsenic (As) concentrations in DCB-extracts with no P addition were significantly higher than those with P fertilization. Arsenic was highly sequestrated in iron plaque; arsenic concentration in iron was up to nearly 120 mg kg(-1), while arsenic concentrations in roots were just several mg kg(-1). Both arsenic and phosphate concentrations in iron plaque were highly positively correlated with the amounts of iron plaque (DCB-extractable Fe). Contrary to normal understanding that increasing P supply could reduced As accumulation in plants, results from the present study showed that P fertilization did not inhibit the As uptake by plants (As accumulation in aboveground), which was probably due to the fact that iron plaque formation was improved under low P conditions, thus leading to more As sequestration in the iron plaque. Thus results obtained in this study indicated that the iron plaque may inhibit the transfer of As from roots to shoots, and thus alter the P-As interaction in plant As uptake processes.

Arsenic↗
PubMed2005

Quantification of water uptake by arbuscular mycorrhizal hyphae and its significance for leaf growth, water relations, and gas exchange of barley subjected to drought stress.

Arbuscular mycorrhizal fungi alleviate drought stress in their host plants via the direct uptake and transfer of water and nutrients through the fungal hyphae to the host plants. To quantify the contribution of the hyphae to plant water uptake, a new split-root hyphae system was designed and employed on barley grown in loamy soil inoculated with Glomus intraradices under well-watered and drought conditions in a growth chamber with a 14-h light period and a constant temperature (15 degrees C; day/night). Drought conditions were initiated 21 days after sowing, with a total of eight 7-day drying cycles applied. Leaf water relations, net photosynthesis rates, and stomatal conductance were measured at the end of each drying cycle. Plants were harvested 90 days after sowing. Compared to the control treatment, the leaf elongation rate and the dry weight of the shoots and roots were reduced in all plants under drought conditions. However, drought resistance was comparatively increased in the mycorrhizal host plants, which suffered smaller decreases in leaf elongation, net photosynthetic rate, stomatal conductance, and turgor pressure compared to the non-mycorrhizal plants. Quantification of the contribution of the arbuscular mycorrhizal hyphae to root water uptake showed that, compared to the non-mycorrhizal treatment, 4 % of water in the hyphal compartment was transferred to the root compartment through the arbuscular mycorrhizal hyphae under drought conditions. This indicates that there is indeed transport of water by the arbuscular mycorrhizal hyphae under drought conditions. Although only a small amount of water transport from the hyphal compartment was detected, the much higher hyphal density found in the root compartment than in the hyphal compartment suggests that a larger amount of water uptake by the arbuscular mycorrhizal hyphae may occur in the root compartment.

Circadian Rhythm↗
PubMed2005

Cyclophosphamide induces mRNA, protein and enzyme activity of cytochrome P450 in rat.

The effects of cyclophosphamide (CPA) on CYP enzymes in vivo and its auto induction in rat were investigated in Wistar/Fu male rats at a single dose (40 or 200 mg kg(-1)) or as repeated dose of 200 mg kg(-1) CPA. After a single dose of CPA, mRNAs of CYPs 2B1, 2B2, 3A2, 2C11 were significantly induced up to 220-, 6.7-, 5.0- and 5.8-fold at the low dose CPA, and 4800-, 52-, 22- and 2.5-fold at the high dose. CYP2B1/2 and CYP3A proteins were increased by 4- and 2-fold (low dose) and by 28- and 1.7-fold (high dose). CYP2C11 protein levels were not altered. Microsomal activities of CYP2B, CYP3A and 2C11 were increased by 2-, 1.8- and 1.3-fold at low dose CPA, and 3.2-, 1.7- and 1.6-fold at high dose. A significant (p<0.05) decrease in CPA concentration and a significant (p<0.05) increase in 4-OH-CPA levels were observed with repeated administration of CPA. Acute induction effect on CYP2B1, 2B2, 2C11 and 3A2 and a substantial up regulation of CYP2B1 mRNA were observed after a single dose of CPA, auto induction was observed by repeated administration.

Animals↗
PubMed2005

GnRH-I and GnRH-II have differential modulatory effects on human peripheral blood mononuclear cell proliferation and interleukin-2 receptor gamma-chain mRNA expression in healthy males.

GnRH-I and its receptor (GnRHR-I) have previously been demonstrated and shown to be biologically active in the immune system, notably within peripheral lymphocytes. Recently however, a second form of GnRH (GnRH-II) has been described in the human. The functions of both these neuropeptides in PMBCs have not been understood yet. The present study was therefore designed to investigate the effects of GnRH-I and/or GnRH-II on human PMBC proliferation in males. Secondly, the effects of GnRH-I and GnRH-II on IL-2 dependent lymphocyte proliferation were examined. Finally, we analysed the role of GnRH-I and GnRH-II in IL-2R gamma-chain expression. Peripheral venous blood samples were obtained from six male healthy volunteers (Mean age 27.75 +/- 1.5). Non-radioactive cell proliferation assay was used for proliferation studies and we used quantitative real-time RT-PCR to examine the role of GnRH-I and GnRH-II on IL-2R gamma-chain expression in PMBCs. Treatment of PMBCs with GnRH-I (10(-9) M and 10(-5) M) and with interleukin-2 (IL-2) (50 U/ml) resulted in a significant increase in cell proliferation compared with the untreated control. PMBCs cotreated with IL-2 and GnRH-I demonstrated higher proliferative responses than IL-2 treatment alone, the enhancement of GnRH-I on IL-2 response being significant only at GnRH-I concentration of 10(-5) M. Co-incubation of IL-2+ GnRH 10(-5) M with a GnRH antagonist (Cetrorelix; 10(-6) M) significantly decreased the proliferation. GnRH-II did not affect the proliferation of PMBCs alone, and did not alter the proliferative response to IL-2. The proliferative responses to GnRH-I (alone and with IL-2) were significantly attenuated by GnRH-II coincubation (each in equal molar concentrations; 10(-9) M to 10(-5) M). It was found that GnRH-I increased the expression of IL-2Rgamma mRNA in a dose dependent manner, with a significant increase of percentage 162.3 +/- 14 of control at 10(-5) M. In contrast, IL-2Rgamma expression was significantly decreased in all concentrations of GnRH-II (10(-9) M to10(-5) M), and the maximum decrease was detected at 10(-5) M, with percentage 37.7 +/- 6.6 of control. All these findings strongly suggest that regulation of IL-2R expression may therefore be an important target for GnRH-I and GnRH-II in PMBCs in males. In summary, present study clearly demonstrates the differential effects of GnRH-I and GnRH-II on PMBC proliferation, IL-2 proliferative response, and IL-2Rgamma expression in PMBCs in males. To our knowledge, our observations provide the first evidence for the interactions of these local neuropeptides at lymphocyte level. Further experimental data in human are warranted to explore the clinical implications of these data.

Adult↗
PubMed2005

Type II collagen and aggrecan mRNA expressions in rabbit condyle following disc displacement.

The aim of this investigation was to study the remodelling of cartilage in the mandibular condyle following disc displacement (DD) of the temporomandibular joint (TMJ). Forty adult Japanese white rabbits were used in this study. The right joints of 28 of the 40 rabbits had their discs surgically displaced. Four of the 28 were killed at 4 days or 1, 2, 4, 6, 8 and 12 weeks after surgery. The messenger RNA (mRNA) expression levels of aggrecan and type II collagen in cartilages were measured using in situ hybridization techniques. Results showed that aggrecan mRNA expression reduced in the first week after DD. The expression began to recover after 4 weeks and reached a normal level after 6 weeks. Type II collagen mRNA expression reduced from 4 weeks and the expression recovered after 8 weeks. This suggests that the chondrocyte reacting to the displacement of the TMJ disc, alters its matrix gene expression patterns and it is may be the cause of the shape changes of TMJ after DD.

Aggrecans↗
PubMed2004

Biomechanical and electromyographic evaluation of ankle foot orthosis and dynamic ankle foot orthosis in spastic cerebral palsy.

This study evaluated the biomechanical and electromyographic effects of conventional ankle foot orthoses (AFOs) and dynamic ankle foot orthoses (DAFOs) on gait in patients with spastic cerebral palsy (CP). Thirteen patients with dynamic equinus underwent motion analysis with electromyography. Both AFOs and DAFOs provided longer stride length, permitted pre-positioning for initial contact, and successfully controlled the excessive plantarflexion during the swing phase. Median frequency (MF) of EMG signal indicated that extremely high firing was found in the patient's lower limbs compared to controls that resulted in tiredness. The DAFOs allowed a significantly larger total ankle range of motion than the AFOs. However, AFOs significantly reduced the MF while DAFOs did not. The reduced MF seen when wearing AFOs suggested an improvement of walking endurance. The DAFO had the advantage of less restriction on ankle movement, which avoids muscular atrophy and improves orthotic compliance.

Ankle Joint↗
PubMed2004

Identification and molecular characterization of a novel y-type Glu-Dt 1 glutenin gene of Aegilops tauschii.

A novel y-type high-molecular-weight glutenin subunit possessing a slightly faster mobility than that of subunit 1Dy12 in SDS-PAGE, designated 1Dy12.1(t) in Aegilops tauschi, was identified by one- and two-dimensional gel and capillary electrophoresis. Its coding gene at the Glu-D(t) 1 locus was amplified with allele-specific-PCR primers, and the amplified products were cloned and sequenced. The complete nucleotide sequence of 2,807 bp containing an open reading frame of 1,950 bp and 857 bp of upstream sequence was obtained. A perfectly conserved enhancer sequence and the -300 element were present at positions of 209-246 bp and 424-447 bp upstream of the ATG start codon, respectively. The deduced mature protein of 1 Dy12.1(t) subunit comprised 648 amino acid residues and had a Mr of 67,518 Da, which is slightly smaller than the 1Dy12 (68,695 Da) but larger than the 1Dy10 (67,495 Da) subunits of bread wheat, respectively, and corresponds well with their relative mobilities when separated by acid-PAGE. The deduced amino acid sequence indicated that the 1Dy12.1(t) subunit displayed a greater similarity to the 1Dy10 subunit, with only seven amino acid substitutions, suggesting that this novel gene could have positive effect on bread-making quality. A phenetic tree produced by nucleotide sequences showed that the x- and y-type subunit genes were respectively clustered together and that the Glu-D(t) 1y12.1 gene of Ae. tauschii is closely related to other y-type subunit genes from the B and D genomes of hexaploid bread wheat.

Agriculture↗
PubMed2004

Prothrombin Shanghai: hypoprothrombinaemia caused by substitution of Gla29 by Gly.

Prothrombin deficiency is a rare bleeding disorder inherited as an autosomal recessive trait. In this study, we reported a Chinese family with hereditary prothrombin deficiency. The proposita had a prolonged activated partial thromboplastin time (APTT, 71.6 s) and prothrombin time (PT, 28.0 s). The coagulation factors activities were normal except that prothrombin coagulation activity was markedly reduced, and the prothrombin antigen level was moderately decreased. Nucleotide sequencing of amplified DNA revealed a novel mutation, Glu (GAG) to Gly (GGG) at residue 29, which normally undergoes gamma-carboxylation within the Gla domain of prothrombin. The proposita was identified as homozygous, while her father, mother and maternal grandmother were heterozygous for the mutation. Gla29 has been demonstrated as one of the key residue for Ca2+-binding, membrane interaction and biological activity of prothrombin.

Amino Acid Substitution↗
PubMed2004

Relationship between serum testosterone and activities of testicular enzymes after continuous and intermittent training in male rats.

To gain more information on the effects of training types on testosterone secretion, the present study investigated the relationship between serum testosterone (ST) and the activities of oxydoreductive enzymes in Leydig cells to continuous and intermittent training regimes. Male rats swam with a load of 3.5 % body weight for 90 min in the continuous training group, and 15 min separated by a 7-min rest interval x 6 times in the intermittent training group, 6 days per week for 5 weeks. ST were measured immediately and 24 h after exercise, and the activities of SDH, LDH and G6PDH in Leydig cells were measured 24 h after exercise, following 5 weeks of training. It was found that ST declined following continuous (0.54 +/- 0.32 nmol/l) and intermittent (1.64 +/- 1.80 nmol/l) exercise compared to sedentary group (9.55 +/- 5.17 nmol/l). This diminishing effect on ST was still significant 24 h after continuous exercise (5.96 +/- 2.79 nmol/l), not after intermittent exercise (7.41 +/- 4.77 nmol/l). The activities of SDH and LDH increased, whereas G6PDH decreased in Leydig cells, after both continuous and intermittent training. SDH and G6PDH showed the high activities in the intermittent training group relative to continuous training group. These differences in the activities of SDH and G6PDH might be considered as the possible causes for ST responses to training types.

Animals↗
PubMed2004

Expression of gonadotropin-releasing hormone type-I (GnRH-I) and type-II (GnRH-II) in human peripheral blood mononuclear cells (PMBCs) and regulation of B-lymphoblastoid cell proliferation by GnRH-I and GnRH-II.

GnRH-I and its receptor (GnRHR-I) have previously been demonstrated and shown to be biologically active in the immune system, notably within T cells. Recently however a second form of GnRH (GnRH-II) has been described in the human. The function of both these neuropeptides in B lymphocytes has not previously been explored. The present study investigates GnRH-I and GnRH-II expression in human peripheral mononuclear blood cells (PMBCs) and B lymphoblastoid cells (B-LCLs), as well as their action in regulating B-LCL proliferation in the presence and absence of interleukin-2 (IL-2), both in GnRHR-I mutated lymphocytes and in a normal control. RT-PCR and immunocytochemistry identified locally produced GnRH-I and GnRH-II in all cell groups. Treatment of normal B-LCLs with GnRH-I (10 (-9) M and 10 (-5) M) or with interleukin-2 (IL-2) (50 IU/ml) resulted in a significant increase in cell proliferation compared with the untreated control. IL-2 and GnRH-I (10 (-7) M, 10 (-6) M, 10 (-5) M) induced greater proliferation in normal B-LCLs than IL-2 treatment alone. No significant proliferation occurred in GnRHR-I defective B-LCLs, in response to either GnRH-I (10 (-9) and 10 (-5) M) or IL-2 treatment, nor to IL-2 and GnRH-I (10 (-10) to 10 (-5) M) co-treatment when compared to controls. Co-incubation of IL-2 and IL-2 + GnRH 10 (-5) M with a GnRH antagonist (Cetrorelix; 10 (-6) M) significantly attenuated the proliferation in normal B-LCLs. GnRH-II did not affect proliferation of normal B-LCLs alone, and did not alter the proliferative response to IL-2. Further investigation is required to clarify the physiological relevance of local GnRH-I/GnRH-II in immune system responsiveness.

Adult↗
PubMed2004

CYP2C subfamily, primarily CYP2C9, catalyses the enantioselective demethylation of the endocrine disruptor pesticide methoxychlor in human liver microsomes: use of inhibitory monoclonal antibodies in P450 identification.

1. The endocrine disruptor pesticide methoxychlor undergoes O-demethylation by mammalian liver microsomes forming chiral mono-phenolic (1,1,1-trichloro-2-(4-hydroxyphenyl)-2-(4-methoxyphenyl)ethane, i.e. mono-OH-M) and achiral bis-phenolic oestrogenic metabolites. Human liver microsomes (HLM) generated primarily the S-mono-OH-M. 2. Inhibitory monoclonal antibodies (MAb) identified those P450s catalysing the enantioselective O-demethylation of methoxychlor. In HLM, O-demethylation was inhibited by MAb anti-2C9 (30-40%), diminishing the per cent of S-mono-OH-M from about 80 to 55-60%. MAb anti-CYP1A2, 2A6, 2B6, 2C8, 2C19, 2D6 and 3A4 did not affect the demethylation rate in HLM. Nevertheless, MAb anti-CYP1A2 decreased the formation of R-mono-OH-M from 21-23 to 10-17%, indicating that CYP1A2 exhibits a role in generating the R-enantiomer. 3. Among cDNA-expressed human P450s (supersomes), CYP2C19 was the most active in demethylation, but in HLM, CYP2C19 appeared inactive (no inhibition by MAb anti-CYP2C19). There was a substantial difference in the per cent inhibition of demethylation by MAb anti-CYP2C9 and anti-rat CYP2C (MAb inhibiting all human CYP2C forms) and in altering the enantioselectivity, suggesting that demethylation by combined CYP2C8, 2C18 and 2C19 was significant (20-30%). 4. Polymorphism of methoxychlor demethylation was examined with supersomes and HLM-expressing CYP2C9 allelic variants. CYP2C9*1 and 2C9*2 were highly active; however, CYP2C9*3 appeared inactive.

Alleles↗
PubMed2004

Modulation of the antibody response by Porphyromonas gingivalis and Fusobacterium nucleatum in a mouse model.

Successive immunization of mice with Fusobacterium nucleatum and Porphyromonas gingivalis has been shown to modulate the specific serum IgG responses to these organisms. The aim of this study was to investigate these antibody responses further by examining the IgG subclasses induced as well as the opsonizing properties of the specific antibodies. Serum samples from BALB/c mice immunized with F. nucleatum (gp1-F), P. gingivalis (gp2-P), P. gingivalis followed by F. nucleatum (gp3-PF) F. nucleatum followed by P. gingivalis (gp4-FP) or saline alone (gp5-S) were examined for specific IgG1 (Th2) and IgG2a (Th1) antibody levels using an ELISA and the opsonizing properties measured using a neutrophil chemiluminescence assay. While IgG1 and IgG2a subclasses were induced in all immunized groups, there was a tendency towards an IgG1 response in mice immunized with P. gingivalis alone, while immunization with F. nucleatum followed by P. gingivalis induced significantly higher anti-P. gingivalis IgG2a levels than IgG1. The maximum light output due to neutrophil phagocytosis of P. gingivalis occurred at 10 min using nonopsonized bacteria. Chemiluminescence was reduced using serum-opsonized P. gingivalis and, in particular, sera from P. gingivalis-immunized mice (gp2-P), with maximum responses occurring at 40 min. In contrast, phagocytosis of immune serum-opsonized F. nucleatum demonstrated peak light output at 10 min, while that of F. nucleatum opsonized with sera from saline injected mice (gp5-S) and control nonopsonized bacteria showed peak responses at 40 min. The lowest phagocytic response occurred using gp4-FP serum-opsonized F. nucleatum. In conclusion, the results of the present study have demonstrated a systemic Th1/Th2 response in mice immunized with P. gingivalis and/or F. nucleatum with a trend towards a Th2 response in P. gingivalis-immunized mice and a significantly increased anti-P. gingivalis IgG2a (Th1) response in mice immunized with F. nucleatum prior to P. gingivalis. Further, the inhibition of neutrophil phagocytosis of immune serum-opsonized P. gingivalis was modulated by the presence of anti-F. nucleatum antibodies, while anti-P. gingivalis antibodies induced an inhibitory effect on the phagocytic response to F. nucleatum.

Animals↗
PubMed2004

Sexual and physical abuse are not associated with rectal hypersensitivity in patients with irritable bowel syndrome.

BACKGROUND: Patients with irritable bowel syndrome (IBS) have reduced pain thresholds for rectal distension. In addition, the prevalence of sexual/physical abuse in referred IBS patients is high and is associated with greater pain reporting, poorer health status, and poorer outcome. This lead to a hypothesis that abuse history may sensitise patients to report pain at a lower threshold. AIM: To compare rectal pain thresholds in women with IBS who had a history of severe abuse to IBS women with no history of abuse. METHODS: We studied 74 IBS patients with a history of severe physical and/or sexual abuse and 85 patients with no history of abuse. Abuse history was assessed by a previously validated self-report abuse screening questionnaire. Rectal sensory thresholds were assessed using an electronic barostat and determined by the ascending method of limit (AML) and by the tracking technique. RESULTS: IBS patients with a history of severe abuse had significantly higher rectal pain thresholds, as measured by AML (F (1, 111) = 6.06; p = 0.015) and the tracking technique (F (1, 109) = 5.21; p = 0.024). Patients with a history of severe abuse also reported a significantly higher threshold for urgency to defecate (F (1, 113) = 11.23; p =.001). CONCLUSION: Severe sexual/physical abuse is associated with higher urge and pain thresholds for rectal distension in IBS patients. This suggests that the greater pain reporting and poorer health status in IBS patients with abuse history are not related to increased rectal pain sensitivity. Further studies are needed to determine the causes of these findings.

Adult↗
PubMed2003

Identification of a novel structural interaction in Columnea latent viroid.

Pairwise sequence comparisons suggest that Columnea latent viroid (CLVd) may have originated from a recombination event involving Potato spindle tuber viroid (PSTVd) and Hop stunt viroid (HSVd). To examine the role of specific structural features in determining the host range of CLVd, we constructed a series of interspecific chimeras by replacing increasing portions of its terminal left and pathogenicity domains with the corresponding portions of PSTVd. Exchanges involving the left side of the pathogenicity domain led to lower rates of progeny accumulation in tomato, but one of the resulting chimeras was still able to replicate in cucumber. Exchanges involving the right side of the pathogenicity domain severely inhibited replication in tomato and appeared to abolish replication in cucumber. To identify potential interactions between nucleotides comprising the right side of the pathogenicity domain and other portions of CLVd, melting behaviors of circularized CLVd and PSTVd RNA transcripts were compared using a combination of temperature gradient gel electrophoresis and structural calculations. These analyses revealed an unexpected complementarity between the upper portion of the pathogenicity and terminal right domains of CLVd that facilitates breakdown of the rod-like native structure and formation of secondary hairpin II. Unlike secondary hairpin II, CLVd hairpin IV appears likely to act within the context of the genomic RNA.

Base Sequence↗
PubMed2003

Efficient multipoint mapping: making use of dominant repulsion-phase markers.

The paper is devoted to the problem of multipoint gene ordering with a particular focus on "dominance" complication that acts differently in conditions of coupling-phase and repulsion-phase markers. To solve the problem we split the dataset into two complementary subsets each containing shared codominant markers and dominant markers in the coupling-phase only. Multilocus ordering in the proposed algorithm is based on pairwise recombination frequencies and using the well-known travelling salesman problem (TSP) formalization. To obtain accurate results, we developed a multiphase algorithm that includes synchronized-marker ordering of two subsets assisted by re-sampling-based map verification, combining the resulting maps into an integrated map followed by verification of the integrated map. A new synchronized Evolution-Strategy discrete optimization algorithm was developed here for the proposed multilocus ordering approach in which common codominant markers facilitate stabilization of the marker order of the two complementary maps. High performance of the employed algorithm allows systematic treatment for the problem of verification of the obtained multilocus orders, based on computing-intensive bootstrap and jackknife technologies for detection and removing unreliable marker scores. The efficiency of the proposed algorithm was demonstrated on simulated and real data.

Algorithms↗