[Prevalence of mountain-zoonotic type visceral leishmaniasis in Yangquan City of Shanxi Province from 2015 to 2020]

OBJECTIVE

To investigate the prevalence of mountain-type zoonotic visceral leishmaniasis (MT-ZVL) in Yangquan City, Shanxi Province from 2015 to 2020, so as to provide the scientific evidence for formulating the MT-ZVL control strategy.

METHODS

The epidemiological data pertaining to MT-ZVL cases in Yangquan City from 2015 to 2020 were collected and descriptively analyzed. A Joinpoint regression model was created to analyze the trend in the MT-ZVL incidence in Yangquan City from 2015 to 2020 using annual percent change (APC). The sandflies surveillance data and the prevalence of Leishmania infections in dogs were collected in Yangquan City in 2020, and the regional distribution of sandflies density and sero-prevalence of Leishmania infections in dogs were calculated. In addition, the associations of sandflies density and sero-prevalence of Leishmania infections in dogs with the incidence of human MT-ZVL were examined using the linear correlation analysis.

RESULTS

A total of 162 MT-ZVL cases were reported in Yangquan City, Shanxi Province from 2015 to 2020, with annual mean incidence of 1.9/10⁵, and there were 4, 7, 16, 27, 33 cases and 75 cases with MT-ZVL reported from 2015 to 2020, appearing a tendency towards a rapid rise (APC = 72.79%, t = 11.10, P < 0.01). MT-ZVL cases were reported across the five counties (districts) of Yangquan City, and the cases predominantly occurred in Jiaoqu District (35.2%, 57/162) and Pingding County (33.3%, 54/162). MT-ZVL cases were predominantly detected in residents at ages of 15 years and older (71.6%, 116/162) and at ages of 0 to 2 years (22.2%, 36/162), with farmers (37.4%, 61/162) and diaspora children (24.5%, 40/162) as predominant occupations. The mean density of Phlebotomus chinensis was 6.3 sandflies per trap per night in Yangquan City from during the period from May to September, 2020, with the highest density observed in Jiaoqu District (12.6 sandflies per trap per night) and the lowest in Yuxian County (1.1 sandflies per trap per night), and there was a region-specific mean density of Ph. chinensis in Yangquan City (H = 17.282, P < 0.01). The sero-prevalence of serum anti-Leishmania antibody was 7.4% (2 996/40 573) in domestic dogs in Yangquan City, with the highest sero-prevalence seen in Jiaoqu District (16.6%, 1 444/8 677), and the lowest in Yuxian County (2.3%, 266/11 501), and there was a region-specific sero-prevalence rate of anti-Leishmania antibody in domestic dogs in Yangquan City (χ² = 1 753.74, P < 0.01). The sero-prevalence of anti-Leishmania antibody was significantly higher in stray dogs (20.0%, 159/794) than in domestic dogs (χ² = 176.63, P < 0.01). In addition, there were significant associations among the sandflies density, sero-prevalence of anti-Leishmania antibody in domestic dogs and the incidence of human MT-ZVL (r = 0.832 to 0.870, all P values < 0.05).

CONCLUSIONS

The prevalence of MT-ZVL appeared a tendency towards a rapid rise in Yangquan City from 2015 to 2020, and systematic interventions are urgently needed for MT-ZVL control.

[Prediction of trends for fine-scale spread of Oncomelania hupensis in Shanghai Municipality based on supervised machine learning models]

OBJECTIVE

To predict the trends for fine-scale spread of Oncomelania hupensis based on supervised machine learning models in Shanghai Municipality, so as to provide insights into precision O. hupensis snail control.

METHODS

Based on 2016 O. hupensis snail survey data in Shanghai Municipality and climatic, geographical, vegetation and socioeconomic data relating to O. hupensis snail distribution, seven supervised machine learning models were created to predict the risk of snail spread in Shanghai, including decision tree, random forest, generalized boosted model, support vector machine, naive Bayes, k-nearest neighbor and C5.0. The performance of seven models for predicting snail spread was evaluated with the area under the receiver operating characteristic curve (AUC), F1-score and accuracy, and optimal models were selected to identify the environmental variables affecting snail spread and predict the areas at risk of snail spread in Shanghai Municipality.

RESULTS

Seven supervised machine learning models were successfully created to predict the risk of snail spread in Shanghai Municipality, and random forest (AUC = 0.901, F1-score = 0.840, ACC = 0.797) and generalized boosted model (AUC= 0.889, F1-score = 0.869, ACC = 0.835) showed higher predictive performance than other models. Random forest analysis showed that the three most important climatic variables contributing to snail spread in Shanghai included aridity (11.87%), ≥ 0 °C annual accumulated temperature (10.19%), moisture index (10.18%) and average annual precipitation (9.86%), the two most important vegetation variables included the vegetation index of the first quarter (8.30%) and vegetation index of the second quarter (7.69%). Snails were more likely to spread at aridity of < 0.87, ≥ 0 °C annual accumulated temperature of 5 550 to 5 675 °C, moisture index of > 39% and average annual precipitation of > 1 180 mm, and with the vegetation index of the first quarter of > 0.4 and the vegetation index of the first quarter of > 0.6. According to the water resource developments and township administrative maps, the areas at risk of snail spread were mainly predicted in 10 townships/subdistricts, covering the Xipian, Dongpian and Tainan sections of southern Shanghai.

CONCLUSIONS

Supervised machine learning models are effective to predict the risk of fine-scale O. hupensis snail spread and identify the environmental determinants relating to snail spread. The areas at risk of O. hupensis snail spread are mainly located in southwestern Songjiang District, northwestern Jinshan District and southeastern Qingpu District of Shanghai Municipality.

[Comparison of follow-up treatment regimens for colorectal cancer liver metastases without objective response to neoadjuvant chemotherapy: direct surgery or surgery after second-line chemotherapy]

Objective: To compare the effect of direct surgery or surgery after second-line chemotherapy for colorectal cancer patients with liver metastases who did not achieve objective remission after neoadjuvant chemotherapy. Methods: A retrospective case cohort study was used. The clinical and pathological data of 107 patients with colorectal cancer liver metastases who did not achieve objective response to neoadjuvant chemotherapy at Department of Hepatobiliary Surgery,Cancer Hospital,Chinese Academy of Medical Sciences from December 2008 to December 2016 were retrospectively collected. There were 71 males and 36 females, median age was 57 years (range: 28 to 79 years). According to the different treatment regimens after neoadjuvant chemotherapy,107 cases were divided into a direct surgery group (direct group,n=65) and an operation after receiving second-line chemotherapy group (second-line group,n=42). The propensity score matching(PSM) of the Logistic regression model was used to match the bilobar distribution of liver metastases and the number of first-line chemotherapy cycles in the two groups of patients. The caliper value was set to 0.10 and the matching ratio was 1∶2. T test, Mann-Whitney U test, χ² test or Fisher's exat test was used to analyzed the data between the tuo groups, respectively. Survival analysis design was used to investigate the difference in prognosis between the two groups of patients. Results: The follow-up time(M(IQR)) was 56.3(34.3) months (range: 2.1 to 95.0 months),and all patients were followed up. After PSM,there were 28 cases in the direct group and 42 cases in the second-line group, there were no significant differences in whether R0 resection was feasible,blood loss,blood transfusion,postoperative complications and postoperative hospital stay between the two groups (all P>0.05). The 1,3,and 5-year progression-free survival(PFS) rates of the direct group were 40.0%,16.5%,and 11.0%,and the 1,3,and 5-year overall survival(OS) rates were 98.5%,61.2%,and 41.4%,respectively, the second-line group 1,3,5 years PFS rates were 35.7%,14.3%,14.3%,1,3,5-year OS rate were 95.2%,55.1%,44.4%,respectively. The median PFS time of the direct group and the second-line group was 8.5 months and 7.5 months,respectively,and the difference was not statistically significant (P=0.826). The median OS time of the direct group and the second-line group were 33.8 months and 46.9 months,respectively. The difference was not statistically significant(P=0.646).The median PFS time of the direct group and second-line chemotherapy complete remission and partial remission group(CR/PR group) was 10.2 months and 9.1 months,respectively,and the difference was not statistically significant(P=0.669). The median OS time of the direct group and the second-line CR/PR group was 51.0 months and 46.9 months,respectively,and the difference was not statistically significant(P=0.427). The results of survival analysis suggested that major liver resection was an independent prognosis factor for PFS (HR=1.809,95%CI: 1.067 to 3.067,P=0.028) and OS(HR=2.751,95%CI: 1.317 to 5.747,P=0.007). Second-line chemotherapy was not an independent prognostic factor for PFS (HR=0.945, 95%CI:0.570 to 1.567,P=0.828) and OS (HR=0.866,95%CI: 0.468 to 1.602,P=0.646). Conclusions: There is no significant difference in the short-term outcome and long-term prognosis between direct surgery patients and second-line chemotherapy followed by surgery. Second-line chemotherapy is not an independent prognostic factor for colorectal cancer liver metastases patients who fail to achieve objective response after neoadjuvant chemotherapy.

First Report of Leaf Spot Disease Caused by Exserohilum rostratum on Pineapple in Hainan Province, China

Pineapple (Ananas comosus (L.) Merr.) is an important perennial monocotyledonous plant that serves as an important fruit crop globally and is also produced in the Hainan Province of China where production in 2009 was 296,600 t. In July 2009, atypical symptoms of a leaf spot disease were observed on mature pineapple leaves in Chengmai County; approximately 15% of plants propagated from suckers became symptomatic after 150 to 300 days, eventually causing a 3 to 10% yield loss. In the initial infection stage, grayish white-to-yellowish white spots emerged on the leaf surfaces that ranged from 1.0 to 2.4 × 0.3 to 0.7 cm; black specks were not always present in the spots. Leaf spots also had distinctive light brown-to-reddish brown banding pattern on the edges. Several spots would often merge to form large lesions, 6.5 to 15.4 × 2.5 to 5.6 cm, covering more than 67% of the leaf surface, which can lead to death of the plant. Infected pineapple leaves collected from an orchard of Chengmai County were surface sterilized (75% ethanol for 30 s, 0.1% HgCl₂ for 2 min, and rinsed three times in sterile distilled water). Leaf pieces were placed on potato dextrose agar medium and then incubated at 25°C. The emerging fungal colonies were grayish white to brown. Similar strains were obtained from Qionghai City and Wanning City subsequently. Two isolates, ITF0706-1 and ITF0706-2, were used in confirmation of the identity of the pathogen and in pathogenicity tests. Colonies were fast growing (more than 15 mm per day at 25 to 30°C) with dense aerial mycelia. Conidia were fusiform, pyriform to oval or cylindrical, olive brown to dark brown, 3 to 10 septate (typically 5 to 8), 33.2 to 102.5 × 9.0 to 21.3 μm, with a strongly protruding hilum bulged from the basal cell, which were similar to the Type A conidia described by Lin et al. (3). The strains were subjected to PCR amplification of the internal transcribed spacer (ITS)1-5.8S-ITS2 regions with universal primer pair ITS1/ITS4. The ITS sequence comparisons (GenBank Accession Nos. JN711431 and JN711432) shared between 99.60 and 99.83% identity with the isolate CATAS-ER01 (GenBank Accession No. GQ169762). According to morphological and molecular analysis, the two strains were identified as Exserohilum rostratum (Drechs.) Leonard & Suggs. Pathogenicity experiments were conducted five times and carried out by spraying a conidial suspension (10⁵ CFU/ml) on newly matured leaves of healthy pineapple plants; plants sprayed with sterile water served as the negative control. Plants were incubated in the growth chamber at 20 to 25°C. Symptoms of leaf spot developed on test plants 7 days after inoculation while the control plants remained asymptomatic. Koch's postulates were fulfilled with the reisolation of the two fungal strains. Currently, E. rostratum is one of the most common pathogens on Bromeliads in Florida (2) and has been reported on Zea mays (4), Musa paradisiacal (3), and Calathea picturata (1) in China, but to our knowledge, this is the first report of leaf spot disease caused by E. rostratum on pineapple in Hainan Province of P.R. China. References: (1) L. L. Chern et al. Plant Dis. 95:1033, 2011. (2) R. M. Leahy. Plant Pathol. Circ. No. 393. Florida Department of Agriculture and Consumer Services Division of Plant Industry, 1999. (3) S. H. Lin et al. Australas. Plant Pathol. 40:246, 2011. (4) J. N. Tsai et al. Plant Pathol. Bull. 10:181, 2001.

Why do essential proteins tend to be clustered in the yeast interactome network?

Recently, the debate on the centrality-lethality rule is resolved by the "second-generation" high-throughput Y2H data from the yeast interactome network, which suggests no significant correlation between the degree of connectedness and essentiality of proteins. However, it is still not clear why essential proteins strongly tend to interact with each other. Previously, the concept of essential protein-protein interactions was proposed to explain the mechanism underlying the clustering of essential proteins. In this article we show that 67 to 75% of the excessive interactions between essential proteins (IBEPs) in the yeast interactome network can be attributed to interactions within protein complexes characterised by the same deletion phenotype for subunits within the complex. Furthermore, 20 to 78% of the excess in IBEPs are caused by the strongly modular structure of the network and by variation in protein essentiality among modules. Not only do proteins function as an interactive network in cellular processes, but furthermore, many proteins do not take part in the network alone, but integrate into protein complexes and many functionally related complexes integrate into modules. So, the local structure of protein complexes as both functional and structural modules are the main contributory factors in the clustering of essential proteins.

Impacts of yeast metabolic network structure on enzyme evolution

Vitkup et al. recently presented an analysis of the influence of yeast metabolic network structure on enzyme evolution; different conclusions are reached when modularity is properly accounted for.

A comment on D Vitkup, P Kharchenko and A Wagner: Influence of metabolic network structure and function on enzyme evolution. Genome Biol 2006, 7:R39.

The E-cadherin gene polymorphism 160C->A and cancer risk: A HuGE review and meta-analysis of 26 case-control studies

A single nucleotide polymorphism, - 160C-->A, has been identified in the promoter region of the E-cadherin gene and has been shown to alter its transcriptional activity. To assess susceptibility of -160A allele carriers to seven types of cancers, the authors conducted a comprehensive meta-analysis, up to November 2006, of 26 case-control studies comprising 7,042 cases and 7,011 controls. Pooled odds ratios and 95% confidence intervals were calculated by using the random-effects model. Publication bias, subgroup, and sensitivity analyses were also performed, which showed that -160A allele carriers, compared with noncarriers, had about a 17-19% increased risk of several invasive/metastatic tumors. Analyses of various types of cancers revealed that, in Europeans, the -160AA homozygote was associated with an increased risk of urothelial cancer, carriers of -160A were at increased risk of lung and prostate cancers, and carriers of -160A with gastric cancer were found to suffer a significantly increased risk, whereas their Asian counterparts seemed to be tolerant. No evidence was found that the -160A allele predisposed its carriers to breast, colorectal, or esophageal cancers. These findings indicate that -160A of the E-cadherin gene is emerging as a low-penetrance tumor susceptibility allele for the development of gastric, lung, prostate, and urothelial cancers.

High frequency of level II-V lymph node involvement in RET/PTC positive papillary thyroid carcinoma

AIMS

To investigate the frequency and clinical significance of RET rearrangement in Chinese patients with papillary thyroid carcinoma (PTC) and discuss the role of RET rearrangement in therapeutic decision-making after the performance of level VI lymph node dissection and the 2002 AJCC staging system.

METHODS

RET/PTC-1 and RET/PTC-3 were detected in 126 PTCs using reverse transcription-polymerase chain reaction (RT-PCR) and direct sequencing.

RESULTS

RET rearrangement was detected in 18 cases of PTC. The patient group aged < 20 years had the highest frequency (3/6) of RET rearrangement among the age groups (< 20 years, 20-40 years and > or = 40 years; P=0.03). RET/PTC-1 positive patients were more likely to suffer from Hashimoto's thyroiditis simultaneously (P=0.02) while RET/PTC-3 positive patients had a higher frequency of extrathyroidal extension (P<0.01) and advanced T classification (P<0.01). RET rearrangement (OR=8.70, 95% CI 1.69-44.81), male (OR=3.88, 95% CI 1.41-10.69), age (OR=0.96, 95% CI 0.93-0.99), multifocality (OR=3.54, 95% CI 1.33-9.41) and advanced T classification (OR=7.32, 95% CI 2.91-18.40) were all identified as risk factors of level II-V lymph node involvement in the multivariate analysis.

CONCLUSIONS

The frequency of RET rearrangement in Chinese patients is low and age related. RET/PTC-1 and RET/PTC-3 are associated with different clinical pathological characteristics but not with lymph node involvement. The RET/PTC positive patients should receive more attention to lateral neck in the management of PTC.

SFP genotyping from affymetrix arrays is robust but largely detects cis-acting expression regulators

The recent development of Affymetrix chips designed from assembled EST sequences has spawned considerable interest in identifying single-feature polymorphisms (SFPs) from transcriptome data. SFPs are valuable genetic markers that potentially offer a physical link to the structural genes themselves. However, most current SFP prediction methodologies were developed for sequenced species although SFPs are particularly valuable for species with complex and unsequenced genomes. To establish the sensitivity and specificity of prediction, we explored four methods for identifying SFPs from experiments involving two tissues in two commercial barleys and their doubled-haploid progeny. The methods were compared in terms of numbers of SFPs predicted and their ability to identify known sequence polymorphisms in the features, to confirm existing SNP genotypes and to match existing maps and individual haplotypes. We identified >4000 separate SFPs that accurately predicted the SNP genotype of >98% of the doubled-haploid (DH) lines. They were highly enriched for features containing sequence polymorphisms but all methods uniformly identified a majority of SFPs ( approximately 64%) in features for which there was no sequence polymorphism while 5% mapped to different locations, indicating that "SFPs" mainly represent polymorphism in cis-acting regulators. All methods are efficient and robust at predicting markers for gene mapping.

Genetic dissection of ethanol tolerance in the budding yeast Saccharomyces cerevisiae

Uncovering genetic control of variation in ethanol tolerance in natural populations of yeast Saccharomyces cerevisiae is essential for understanding the evolution of fermentation, the dominant lifestyle of the species, and for improving efficiency of selection for strains with high ethanol tolerance, a character of great economic value for the brewing and biofuel industries. To date, as many as 251 genes have been predicted to be involved in influencing this character. Candidacy of these genes was determined from a tested phenotypic effect following gene knockout, from an induced change in gene function under an ethanol stress condition, or by mutagenesis. This article represents the first genomics approach for dissecting genetic variation in ethanol tolerance between two yeast strains with a highly divergent trait phenotype. We developed a simple but reliable experimental protocol for scoring the phenotype and a set of STR/SNP markers evenly covering the whole genome. We created a mapping population comprising 319 segregants from crossing the parental strains. On the basis of the data sets, we find that the tolerance trait has a high heritability and that additive genetic variance dominates genetic variation of the trait. Segregation at five QTL detected has explained approximately 50% of phenotypic variation; in particular, the major QTL mapped on yeast chromosome 9 has accounted for a quarter of the phenotypic variation. We integrated the QTL analysis with the predicted candidacy of ethanol resistance genes and found that only a few of these candidates fall in the QTL regions.

Average Gene Length Is Highly Conserved in Prokaryotes and Eukaryotes and Diverges Only Between the Two Kingdoms

The average length of genes in a eukaryote is larger than in a prokaryote, implying that evolution of complexity is related to change of gene lengths. Here, we show that although the average lengths of genes in prokaryotes and eukaryotes are much different, the average lengths of genes are highly conserved within either of the two kingdoms. This suggests that natural selection has clearly set a strong limitation on gene elongation within the kingdom. Furthermore, the average gene size adds another distinct characteristic for the discrimination between the two kingdoms of organisms.

Constructing genetic linkage maps under a tetrasomic model

An international consortium has launched the whole-genome sequencing of potato, the fourth most important food crop in the world. Construction of genetic linkage maps is an inevitable step for taking advantage of the genome projects for the development of novel cultivars in the autotetraploid crop species. However, linkage analysis in autopolyploids, the kernel of linkage map construction, is theoretically challenging and methodologically unavailable in the current literature. We present here a theoretical analysis and a statistical method for tetrasomic linkage analysis with dominant and/or codominant molecular markers. The analysis reveals some essential properties of the tetrasomic model. The method accounts properly for double reduction and incomplete information of marker phenotype in regard to the corresponding phenotype in estimating the coefficients of double reduction and recombination frequency and in testing their significance by using the marker phenotype data. Computer simulation was developed to validate the analysis and the method and a case study with 201 AFLP and SSR markers scored on 228 full-sib individuals of autotetraploid potato is used to illustrate the utility of the method in map construction in autotetraploid species.

Novel microdeletion in the transforming growth factor β type II receptor gene is associated with giant and large cell variants of nonsmall cell lung carcinoma

Mutations in the tumor suppressor gene transforming growth factor beta (TGFB) Type II receptor (TGFBR2) are frequently found in many cancers with microsatellite instability, but are less common in lung cancer. In the present study, we looked for mutations in TGFBR2 in nonsmall cell lung carcinoma (NSCLC) cells and tissues. A novel homozygous microdeletion (c.492_507del) was identified in two cell lines derived from the same giant cell carcinoma (GCC) and was confirmed in the corresponding tumor tissues. Furthermore, a heterozygous c.492_507del was found in the germ-line of one patient, as well as in the other GCC cases and some large cell carcinomas (LCC) but not in other subtypes of NSCLC. The 16 bp-microdeletion introduced a premature stop codon at positions 590-592 of the cDNA, resulting in a truncated TGFBR2 protein with a mutated transmembrane domain and loss of kinase domain. The GCC cells were characterized as being unresponsive to TGFB induction both in growth inhibition and stimulation of extracellular matrix protein. Moreover, after the reconstitution of wild-type TGFBR2 expression, the sensitivity to TGFB was restored. Therefore, mutated TGFBR2 seems to play an important role in the abrogation of TGFB signal transduction in GCC cells.

Modeling population genetic data in autotetraploid species

Allozyme and PCR-based molecular markers have been widely used to investigate genetic diversity and population genetic structure in autotetraploid species. However, an empirical but inaccurate approach was often used to infer marker genotype from the pattern and intensity of gel bands. Obviously, this introduces serious errors in prediction of the marker genotypes and severely biases the data analysis. This article developed a theoretical model to characterize genetic segregation of alleles at genetic marker loci in autotetraploid populations and a novel likelihood-based method to estimate the model parameters. The model properly accounts for segregation complexities due to multiple alleles and double reduction at autotetrasomic loci in natural populations, and the method takes appropriate account of incomplete marker phenotype information with respect to genotype due to multiple-dosage allele segregation at marker loci in tetraploids. The theoretical analyses were validated by making use of a computer simulation study and their utility is demonstrated by analyzing microsatellite marker data collected from two populations of sycamore maple (Acer pseudoplatanus L.), an economically important autotetraploid tree species. Numerical analyses based on simulation data indicate that the model parameters can be adequately estimated and double reduction is detected with good power using reasonable sample size.

Divergence Pattern of Duplicate Genes in Protein-Protein Interactions Follows the Power Law

The impact of the biological network structures on the divergence between the two copies of one duplicate gene pair involved in the networks has not been documented on a genome scale. Having analyzed the most recently updated Database of Interacting Proteins (DIP) by incorporating the information for duplicate genes of the same age in yeast, we find that there was a highly significantly positive correlation between the level of connectivity of ancient genes and the number of shared partners of their duplicates in the protein-protein interaction networks. This suggests that duplicate genes with a low ancestral connectivity tend to provide raw materials for functional novelty, whereas those duplicate genes with a high ancestral connectivity tend to create functional redundancy for a genome during the same evolutionary period. Moreover, the difference in the number of partners between two copies of a duplicate pair was found to follow a power-law distribution. This suggests that loss and gain of interacting partners for most duplicate genes with a lower level of ancestral connectivity is largely symmetrical, whereas the "hub duplicate genes" with a higher level of ancient connectivity display an asymmetrical divergence pattern in protein-protein interactions. Thus, it is clear that the protein-protein interaction network structures affect the divergence pattern of duplicate genes. Our findings also provide insights into the origin and development of biological networks.

An improved formulation of marker heterozygosity in recurrent selection and backcross schemes

This report presents a theoretical formulation for predicting heterozygosity of a putative marker locus linked to two quantitative trait loci (QTL) in a recurrent selection and backcross (RSB) scheme. Since the heterozygosity at any given marker locus maintained in such a breeding programme reflects its map location relative to QTL, the present study develops the theoretical analysis of the QTL mapping method that recently appeared in the literature. The formulae take into account selection, recombination and finite population size during the multiple-generation breeding scheme. The single-marker and two-QTL model was compared numerically with the model involving two linked marker loci and two QTL. Without recombination interference, the two models predict the same expected heterozygosity at the linked marker loci, indicating that the model is valid for predicting marker heterozygosity maintained at any loci in an RSB breeding scheme. The formulation is demonstrated numerically for several RSB schemes and its implications in developing a likelihood-based statistical framework for modeling the RSB experiments are discussed.

Theoretical basis for genetic linkage analysis in autotetraploid species

Linkage analysis in autotetraploid species has been an historical challenge in quantitative genetics theory and is a stumbling block that urgently needs to be removed in the rapidly emerging genome research on this species, such as cultivated potato. This article presents theory of a full model of tetrasomic linkage and develops a statistical framework for the linkage analysis. The model considers both double reduction and recombination, the most essential features of tetrasomic inheritance with linked loci, whereas the statistical method takes appropriate account of the major complexities in analyzing both dominant and codominant molecular marker data during map reconstruction in tetraploid species. These complexities include the problems arising from multiple dosage of allelic inheritance, the null allele, allelic segregation distortion, mixed bivalent and quadrivalent pairing in meiosis, and incomplete information of marker phenotype data. The theoretical analysis established the relationship between the coefficients of double reduction at linked loci, which is essential in the present tetrasomic linkage analysis and in assessing the impact of double reduction on the evolution of tetraploid populations. The statistical method, based on the combination of theoretical analysis and a computer-based algorithm, provided analytical tools for predicting the maximum-likelihood estimates of the model parameters. A simulation study showed the feasibility of a practical implementation of the method, detailed the procedure of the analysis, validated the power and reliability in the parameter estimation, and compared the present method with those proposed in the current literature.

Induced recovery of defective membrane expression of a CC chemokine receptor 5 mutant by phytohemagglutinin

CC chemokine receptor 5 (CCR5) is a member of the G-protein-coupled receptor superfamily. It plays an important role in macrophage tropic human immunodeficiency virus-1 entry and in some inflammatory reactions. CCR5-893(-) is a single-nucleotide deletion that results in complete truncation of the C tail of the gene product. We detected CCR5-893(-) in a sample of patients infected with non-tuberculosis mycobacteria and found that it was maintained heterozygously with a frequency of 2%. There is no association between this mutation and any immunodeficiency. Membrane expression of CCR5-893(-) was substantially reduced compared to the wild type, but this defective surface presentation recovered greatly recovered in the presence of 2 mg l(-1) phytohemagglutinin (PHA). However, PHA inducement did not affect the total intracellular expression of CCR5-893(-) or wild-type CCR5. Thus we suggest there exist some PHA-induced factor(s) that could mediate the presentation of truncated CCR5.

TetraploidMap: construction of a linkage map in autotetraploid species

TetraploidMap is a suite of Fortran 90 routines run from Microsoft Windows with a text-based input and output. TetraploidMap enables the user to assemble a linkage map from dominant and codominant (multiallelic) marker loci scored for the parents and full-sib progeny of a cross in an autotetraploid species. It includes routines for the inference of the parental genotypes, identification of linkage groups, two-point analysis to estimate the recombination frequency and LOD score between all pairs of marker in a linkage group, and locus ordering by simulated annealing.

Precision and high-resolution mapping of quantitative trait loci by use of recurrent selection, backcross or intercross schemes

Dissecting quantitative genetic variation into genes at the molecular level has been recognized as the greatest challenge facing geneticists in the twenty-first century. Tremendous efforts in the last two decades were invested to map a wide spectrum of quantitative genetic variation in nearly all important organisms onto their genome regions that may contain genes underlying the variation, but the candidate regions predicted so far are too coarse for accurate gene targeting. In this article, the recurrent selection and backcross (RSB) schemes were investigated theoretically and by simulation for their potential in mapping quantitative trait loci (QTL). In the RSB schemes, selection plays the role of maintaining the recipient genome in the vicinity of the QTL, which, at the same time, are rapidly narrowed down over multiple generations of backcrossing. With a high-density linkage map of DNA polymorphisms, the RSB approach has the potential of dissecting the complex genetic architecture of quantitative traits and enabling the underlying QTL to be mapped with the precision and resolution needed for their map-based cloning to be attempted. The factors affecting efficiency of the mapping method were investigated, suggesting guidelines under which experimental designs of the RSB schemes can be optimized. Comparison was made between the RSB schemes and the two popular QTL mapping methods, interval mapping and composite interval mapping, and showed that the scenario of genomic distribution of QTL that was unlocked by the RSB-based mapping method is qualitatively distinguished from those unlocked by the interval mapping-based methods.

Stability analysis and design of automatic frequency control system for in vivo EPR spectroscopy

Stability analysis and design of an automatic frequency control (AFC) system for in vivo continuous-wave EPR spectroscopy is described. The open-loop function of the feedback control system for the AFC was derived and the stability of the feedback loop systematically examined. A stability analysis of the system is demonstrated and a systematic design procedure is proposed. The design is started from the required system specifications (phase margin, steady-state error, and system bandwidth) and clear guidelines for designing an AFC system are given. A case study of the design is presented based on the specific needs of in vivo EPR measurements. A phase margin of 53 degrees, a steady-state error of 1.6%, and a system bandwidth of up to 1.8 kHz were obtained in the designed AFC system. The system specifications defined in advance are satisfied in this case study.

Modeling linkage disequilibrium between a polymorphic marker locus and a locus affecting complex dichotomous traits in natural populations

Linkage disequilibrium is an important topic in evolutionary and population genetics. An issue yet to be settled is the theory required to extend the linkage disequilibrium analysis to complex traits. In this study, we present theoretical analysis and methods for detecting or estimating linkage disequilibrium (LD) between a polymorphic marker locus and any one of the loci affecting a complex dichotomous trait on the basis of samples randomly or selectively collected from natural populations. Statistical properties of these methods were investigated and their powers were compared analytically or by use of Monte Carlo simulations. The results show that the disequilibrium may be detected with a power of 80% by using phenotypic records and marker genotype when both the trait and marker variants are common (30%) and the LD is relatively high (40-100% of the theoretical maximum). The maximum-likelihood approach provides accurate estimates of the model parameters as well as detection of linkage disequilibrium. The likelihood method is preferred for its higher power and reliability in parameter estimation. The approaches developed in this article are also compared to those for analyzing a continuously distributed quantitative trait. It is shown that a larger sample size is required for the dichotomous trait model to obtain the same level of power in detecting linkage disequilibrium as the continuous trait analysis. Potential use of these estimates in mapping the trait locus is also discussed.

Construction of a genetic linkage map in tetraploid species using molecular markers

This article presents methodology for the construction of a linkage map in an autotetraploid species, using either codominant or dominant molecular markers scored on two parents and their full-sib progeny. The steps of the analysis are as follows: identification of parental genotypes from the parental and offspring phenotypes; testing for independent segregation of markers; partition of markers into linkage groups using cluster analysis; maximum-likelihood estimation of the phase, recombination frequency, and LOD score for all pairs of markers in the same linkage group using the EM algorithm; ordering the markers and estimating distances between them; and reconstructing their linkage phases. The information from different marker configurations about the recombination frequency is examined and found to vary considerably, depending on the number of different alleles, the number of alleles shared by the parents, and the phase of the markers. The methods are applied to a simulated data set and to a small set of SSR and AFLP markers scored in a full-sib population of tetraploid potato.

[Metallic stents for malignant esophageal neoplasms stenosis in advanced stage]

Maligant esophageal stenosis affects the qulity of the patients' life severely. Self-Expanding Metallic Stent (SEMS) can relieve the patient from dysphagia. In this article, we summarized the application and clinical complication of SEMS in maligant esophageal stenosis.

Inferring linkage disequilibrium between a polymorphic marker locus and a trait locus in natural populations

Three approaches are proposed in this study for detecting or estimating linkage disequilibrium between a polymorphic marker locus and a locus affecting quantitative genetic variation using the sample from random mating populations. It is shown that the disequilibrium over a wide range of circumstances may be detected with a power of 80% by using phenotypic records and marker genotypes of a few hundred individuals. Comparison of ANOVA and regression methods in this article to the transmission disequilibrium test (TDT) shows that, given the genetic variance explained by the trait locus, the power of TDT depends on the trait allele frequency, whereas the power of ANOVA and regression analyses is relatively independent from the allelic frequency. The TDT method is more powerful when the trait allele frequency is low, but much less powerful when it is high. The likelihood analysis provides reliable estimation of the model parameters when the QTL variance is at least 10% of the phenotypic variance and the sample size of a few hundred is used. Potential use of these estimates in mapping the trait locus is also discussed.

Anatomical and neurochemical peculiarities of the pika retina: basis for lack of circadian rhythm of core temperature

We have previously reported a complete lack of circadian rhythm in the body temperature of pikas in contrast to other lagomorphs. In this present study, the anatomical and neurochemical findings by immunohistochemical, photo and electron microscopic methods reveal that the photoreceptor system of this animal is poorly developed. This probably explains their stable core body temperature which help them survive in cold temperatures.

Estimating linkage disequilibrium between a polymorphic marker locus and a trait locus in natural populations

Positional cloning of gene(s) underlying a complex trait requires a high-resolution linkage map between the trait locus and genetic marker loci. Recent research has shown that this may be achieved through appropriately modeling and screening linkage disequilibrium between the candidate marker locus and the major trait locus. A quantitative genetics model was developed in the present study to estimate the coefficient of linkage disequilibrium between a polymorphic genetic marker locus and a locus underlying a quantitative trait as well as the relevant genetic parameters using the sample from randomly mating populations. Asymptotic covariances of the maximum-likelihood estimates of the parameters were formulated. Convergence of the EM-based statistical algorithm for calculating the maximum-likelihood estimates was confirmed and its utility to analyze practical data was exploited by use of extensive Monte-Carlo simulations. Appropriateness of calculating the asymptotic covariance matrix in the present model was investigated for three different approaches. Numerical analyses based on simulation data indicated that accurate estimation of the genetic parameters may be achieved if a sample size of 500 is used and if segregation at the trait locus explains not less than a quarter of phenotypic variation of the trait, but the study reveals difficulties in predicting the asymptotic variances of these maximum-likelihood estimates. A comparison was made between the statistical powers of the maximum-likelihood analysis and the previously proposed regression analysis for detecting the disequilibrium.

A mathematical model of adaptive behavior in quadruped locomotion

Locomotion involves repetitive movements and is often executed unconsciously and automatically. In order to achieve smooth locomotion, the coordination of the rhythms of all physical parts is important. Neurophysiological studies have related that basic rhythms are produced in the spinal network called, the central pattern generator (CPG), where some neural oscillators interact to self-organize coordinated rhythms. We present a model of the adaptation of locomotion patterns to a variable environment, and attempt to elucidate how the dynamics of locomotion pattern generation are adjusted by the environmental changes. Recent experimental results indicate that decerebrate cats have the ability to learn new gait patterns in a changed environment. In those experiments, a decerebrate cat was set on a treadmill consisting of three moving belts. This treadmill provides a periodic perturbation to each limb through variation of the speed of each belt. When the belt for the left forelimb is quickened, the decerebrate cat initially loses interlimb coordination and stability, but gradually recovers them and finally walks with a new gait. Based on the above biological facts, we propose a CPG model whose rhythmic pattern adapts to periodic perturbation from the variable environment. First, we design the oscillator interactions to generate a desired rhythmic pattern. In our model, oscillator interactions are regarded as the forces that generate the desired motion pattern. If the desired pattern has already been realized, then the interactions are equal to zero. However, this rhythmic pattern is not reproducible when there is an environmental change. Also, if we do not adjust the rhythmic dynamics, the oscillator interactions will not be zero. Therefore, in our adaptation rule, we adjust the memorized rhythmic pattern so as to minimize the oscillator interactions. This rule can describe the adaptive behavior of decerebrate cats well. Finally, we propose a mathematical framework of an adaptation in rhythmic motion. Our framework consists of three types of dynamics: environmental, rhythmic motion, and adaptation dynamics. We conclude that the time scale of adaptation dynamics should be much larger than that of rhythmic motion dynamics, and the repetition of rhythmic motions in a stable environment is important for the convergence of adaptation.

Detecting linkage disequilibrium between a polymorphic marker locus and a trait locus in natural populations

A novel statistical model was developed to test for linkage disequilibrium between a polymorphic genetic marker locus and a locus underlying a quantitative trait (QTL) in natural populations using principles of analysis of variance of unbalanced data and analysis of regression involving data of non-normal distribution. Powers of these statistical tests are formulated as functions of census population size, allelic frequencies at the marker locus and the trait locus, additive and dominance effects at the QTL as well as the coefficient of linkage disequilibrium. Theoretical predictions of the power are validated by extensive Monte Carlo simulations. Among all these factors examined, the amount of the disequilibrium and the size of effect of the QTL are of most importance in determining the power, and the dominance and the allele frequencies at the two loci have substantial effects on the power. Numerical analyses based upon the theoretical calculations and simulation studies favour use of regression of the number of marker alleles on the trait phenotypes as a measure of detection of linkage disequilibrium. Theoretical analysis is also performed to investigate robustness of the formula for predicting the variance of the regression coefficient, which requires normality of the regression variables, whereas normality may not be strictly warranted.

A population genetics model of marker-assisted selection

A deterministic two-loci model was developed to predict genetic response to marker-assisted selection (MAS) in one generation and in multiple generations. Formulas were derived to relate linkage disequilibrium in a population to the proportion of additive genetic variance used by MAS, and in turn to an extra improvement in genetic response over phenotypic selection. Predictions of the response were compared to those predicted by using an infinite-loci model and the factors affecting efficiency of MAS were examined. Theoretical analyses of the present study revealed the nonlinearity between the selection intensity and genetic response in MAS. In addition to the heritability of the trait and the proportion of the marker-associated genetic variance, the frequencies of the selectively favorable alleles at the two loci, one marker and one quantitative trait locus, were found to play an important role in determining both the short- and long-term efficiencies of MAS. The evolution of linkage disequilibrium and thus the genetic response over several generations were predicted theoretically and examined by simulation. MAS dissipated the disequilibrium more quickly than drift alone. In some cases studied, the rate of dissipation was as large as that to be expected in the circumstance where the true recombination fraction was increased by three times and selection was absent.

Maximum likelihood estimation of linkage between a marker gene and a quantitative trait locus. II. Application to backcross and doubled haploid populations

The algorithm for estimating both the recombination fraction between a marker gene and a locus affecting a quantitative trait, and also the means and variances of the QTL genotypes, is extended to backcross and doubled haploid populations. The simulation experiments show that estimates of these parameters can be obtained with acceptable accuracy and results are compared with those obtained using F2 populations studied previously (Luo & Kearsey, 1989).

Maximum likelihood estimation of linkage between a marker gene and a quantitative locus

A maximum likelihood approach is developed for estimating the recombination fraction in a segregating population (F2), between a marker gene and a locus affecting a quantitative trait as well as estimating the means and variances of the three genotypes of the quantitative trait. The experimental results from computer simulations show that even with experimental sizes of 500, estimates of the parameters can be obtained by aid of the codominant marker gene as long as the heritability of the quantitative trait in question is not less than 0.10. However at low heritabilities the variances of estimates are very large.