Frequencies of functional caspase 12 genotypes in the North Africa population

Caspase 12(Csp-12) is a cysteine protease that plays a role in regulation of cytokine maturation. It is present either in a functional full-length variant (Csp-12L) that predisposes to a lower immune response or in an inactive, common version (Csp-12S) that contains a stop codon that results in a truncated form. Genomic DNA from unrelated North Africans, residents of 4th Nile Cataract Region in Sudan, was analyzed. One hundred umbilical blood samples of Polish newborns served as a reference group from the Caucasian population. The analysis of stop-codon polymorphism performed on the 212 human samples from Northern Sudan identified 6.6% individuals with heterozygous genotypes while not one homozygous Csp-12L was found. All examined Polish individuals were homozygous Csp-12S.     

Caspase-1 activation of caspase-6 in human apoptotic neurons

Active caspase-6 (Csp-6) induces cell death in primary cultures of human neurons and is abundant in the neuropathological lesions of Alzheimer's disease. However, the mode of Csp-6 activation is not known. Here, we show that the Csp-1 inhibitor, Z-YVAD-fmk specifically prevents activation of Csp-6 and cell death in human neurons. A transient increase in Csp-1-like activity and an increase in the p23Csp-1 subunit occur early after serum deprivation. Recombinant active Csp-1 (R-Csp-1) cleaves recombinant and neuronal pro-Csp-6 in vitro resulting in Csp-6 activity. However, R-Csp-1 does not induce cell death when microinjected in human neurons despite the inhibition of serum-deprivation induced cell death with a Csp-1 dominant negative construct. These results show that Csp-1 is an upstream positive regulator of Csp-6-mediated cell death in primary human neurons. Furthermore, these results suggest that the activation of Csp-1 must be accompanied by an apoptotic insult to induce Csp-6-mediated cell death.     

Proteasomal degradation of caspase-6 in 17beta-estradiol-treated neurons

In primary cultures of human neurons, 17beta-estradiol (17beta-E2) prevents caspase-6-mediated cell death and induces a caspase inhibitory factor (CIF) inhibiting active caspase-6 (Csp-6) in vitro. Here, we show that treatment of neurons with 17beta-E2 results in a proteasomal-dependent but ubiquitin-independent degradation of endogenous and exogenous active Csp-6 in live neurons and in cell free assays, respectively. We further show that the proteasomal-dependent degradation of Csp-6 is not required for its inhibition. Using several protease inhibitors, we find that leupeptin, E-64, and ALLN prevent inhibition of recombinant active Csp-6 (R-Csp-6) in 17beta-E2-treated neuronal protein extracts. Because all three protease inhibitors have the ability to inhibit cysteine proteases, we believe that a cysteinyl protease activity may be required for 17beta-E2-mediated inhibition of active Csp-6. However, we exclude caspases, calpains, and cathepsins as potential cysteinyl proteases involved in the 17beta-E2-mediated Csp-6 inhibition. The results suggest that a proteolytic activity inhibited by leupeptin, E-64, and ALLN is needed to inhibit Csp-6 and that the inhibited Csp-6 is subsequently degraded by the proteasome. The mechanism of 17beta-E2-mediated inhibition of Csp-6 is different from the ubiquitin-dependent proteasomal degradation of Csp-3 and Csp-7 by XIAP and cIAP2 but consistent with the mechanism of Baculovirus p35 inhibition of caspases.     

我国草地贪夜蛾田间种群有机磷和氨基甲酸酯类杀虫剂靶标基因ace-1的基因型和突变频率

【目的】对入侵我国的草地贪夜蛾Spodoptera frugiperda有机磷和氨基甲酸酯类杀虫剂靶标基因ace-1的基因型进行分子检测,明确抗性基因频率,进而指导田间科学用药。【方法】采集中国12省份的草地贪夜蛾田间种群幼虫样本,提取单头样本的基因组DNA,利用特异性引物进行PCR扩增,获得ace-1基因片段。根据碱基、氨基酸序列比对和测序峰图分析,明确与有机磷和氨基甲酸酯类杀虫剂抗性相关的3个氨基酸突变位点A201S, G227A和F290V的基因型和抗性基因频率。【结果】通过DNA检测分析中国12省份草地贪夜蛾田间种群589头个体ace-1基因的基因型和突变频率发现,在A201S位点检测到137头个体为抗性杂合基因型,抗性基因频率为11.6%,未发现抗性纯合基因型个体;G227A位点589头个体均为敏感纯合基因型;F290V位点的抗性基因频率最高,达到57.1%,携带抗性基因的个体数量达到523头(占样本总数的88.8%)。【结论】结果表明入侵我国的草地贪夜蛾种群携带高频率的对有机磷和氨基甲酸酯类杀虫剂抗性基因。田间防治建议不用或少用有机磷和氨基甲酸酯类杀虫剂,同时进一步加强田间抗性监测工作。     

A frequent tyrosinase gene mutation associated with type I-A (tyrosinase-negative) oculocutaneous albinism in Puerto Rico.

We have determined the mutations in the tyrosinase gene from 12 unrelated Puerto Rican individuals who have type I-A (tyrosinase-negative) oculocutaneous albinism (OCA). All but one individual are of Hispanic descent. Nine individuals were homozygous for a missense mutation (G47D) in exon I at codon 47. Two individuals were heterozygous for the G47D mutation, with one having a missense mutation at codon 373 (T373K) in the homologous allele and the other having an undetermined mutation in the homologous allele. One individual with negroid features was homozygous for a nonsense mutation (W236X). The population migration between Puerto Rico and the Canary Islands is well recognized. Analysis of three individuals with OCA from the Canary Islands showed that one was a compound heterozygote for the G47D mutation and for a novel missense mutation (L216M), one was homozygous for a missense mutation (P81L), and one was heterozygous for the missense mutation P81L. The G47D and P81L missense mutations have been previously described in extended families in the United States. Haplotypes were determined using four polymorphisms linked to the tyrosinase locus. Haplotype analysis showed that the G47D mutation occurred on a single haplotype, consistent with a common founder for all individuals having this mutation. Two different haplotypes were found associated with the P81L mutation, suggesting that this may be either a recurring mutation for the tyrosinase gene or a recombination between haplotypes.     

Plasma and Urinary Sulfate Determination in a Cohort with Autism

Sulfate is important for mammalian development but is not routinely measured in clinical settings. The renal NaS1 sulfate transporter maintains circulating sulfate levels and is linked to renal sulfate wasting in mice. Some autistic individuals exhibit renal sulfate wasting, but the etiology is yet unknown. We measured plasma and urinary sulfate levels, calculated the fractional excretion index (FEI) of sulfate, and screened for two loss-of-function NaS1 sequence variants (R12X and N174S) in 23 autistic individuals. The FEI sulfate values ranged from 0.13 to 0.50. NaS1 variants were detected in 18 of the 23 individuals (11 heterozygous N174S, four homozygous N174S, two heterozygous R12X, and one individual carried both R12X and N174S). Those individuals with neither sequence variant had FEI sulfate ≤ 0.34, whereas FEI sulfate ≥ 0.35 was found in about 60 % (11 of 18) of individuals that had R12X and/or N174S. This study links renal sulfate wasting with loss-of-function NaS1 sequence variants in humans.     

Visceral leishmaniasis in eastern Sudan: parasite identification in humans and dogs; host-parasite relationships

In 1996, an epidemic outbreak of visceral leishmaniasis (VL) started in Barbar el Fugara, a village in Gedarif State (eastern Sudan). From 1997 to 2000, regular epidemiological studies were carried out in the human population, as well as in mammals and sand flies. In symptomatic patients, 46/69 lymph node, 6/20 post kala-azar dermal leishmaniasis (PKDL) and 1/4 cutaneous cultures in NNN medium were positive. In 69 dogs, 23/79 lymph node cultures were positive. In other mammals (47 rodents, five donkeys, one mongoose and one monkey) spleen and/or blood cultures were negative. Characterization of isolated strains (by starch gel electrophoresis and isoelectrofocusing) identified three zymodemes of Leishmania donovani, two of L. infantum and two of L. archibaldi complexes from patient samples and three zymodemes of L. donovani, three of L. infantum and two of L. archibaldi complexes from dog samples. Five of them were present in both man and dog. For the first time, a strain from a PKDL case was identified as L. infantum, and a child had the same L. infantum zymodeme in VL and in subsequent PKDL. Blood samples from dogs were studied by immunofluorescent antibody test (IFAT). The seroprevalence in dogs was 72.5%, 74.3% and 42.9% in 1998, 1999 and 2000, respectively. By using CDC miniature light traps 12 745 sand flies were collected and then identified. Phlebotomus papatasi (7%) and P. orientalis (5%) were sympatric, mainly inside homes (85% and 75%, respectively). These results, the relative stability of seroprevalence in dogs and the intradomiciliar presence of P. orientalis, known as a vector of VL in Sudan, suggest several hypotheses: (i) man is responsible for the disease in dogs, (ii) the dog is the reservoir of VL, (iii) the dog is an intermediate host between a possible sylvatic cycle and the anthroponotic cycle. More extensive studies are needed to assess the transmission cycle of VL in this area of Sudan.     

Analysis of ribosomal DNA internal transcribed spacer sequences of the Leishmania donovani complex

To understand phylogenetic relationships of species and strains within the Leishmania donovani complex, we have analyzed the ribosomal DNA internal transcribed spacer (ITS) sequences of 27 Leishmania infantum, 2 Leishmania chagasi, 18 L. donovani and 5 Leishmania archibaldi strains of different zymodemes and geographical origin. Eight ITS sequence types were found. All detected sequence variation within ITS1 and ITS2 was based on 12 polymorphic microsatellites. The L. infantum strains from the Mediterranean region, China and L. chagasi from the New World formed a phylogenetic group well separated from the second main group including all strains from East Africa and India. Within the latter group three distinct phylogenetic subgroups could be differentiated: (1) L. donovani (Sudan/Ethiopia, China) + L. archibaldi (Sudan), (2) L. donovani (Sudan/Ethiopia) + L. infantum (Sudan) + L. archibaldi (Sudan/Ethiopia), and (3) L. donovani (Kenya, India). These groups are not consistent with previous species definitions based on isoenzyme analyses, e.g. L. infantum is polyphyletic and L. archibaldi is not supported as a distinct species. Two groups of Indian strains could be differentiated, one of which has an identical sequence type to the strains from Kenya. Three main lineages of strains can thus be differentiated in East Africa: two quite distantly related groups of strains from Sudan/Ethiopia, and a third group including all strains from Kenya, which is more closely related to part of the Indian strains than to any of the Sudanese/Ethiopian groups. The ITS sequence analysis presented here supports the need for revision of the taxonomy of the L. donovani complex.     

Population specificity of the DNAI1 gene mutation spectrum in primary ciliary dyskinesia (PCD)

Background

Mutations in the DNAI1 gene, encoding a component of outer dynein arms of the ciliary apparatus, are the second most important genetic cause of primary ciliary dyskinesia (PCD), the genetically heterogeneous recessive disorder with the prevalence of ~1/20,000. The estimates of the DNAI1 involvement in PCD pathogenesis differ among the reported studies, ranging from 4% to 10%.

Methods

The coding sequence of DNAI1 was screened (SSCP analysis and direct sequencing) in a group of PCD patients (157 families, 185 affected individuals), the first ever studied large cohort of PCD patients of Slavic origin (mostly Polish); multiplex ligation-dependent probe amplification (MLPA) analysis was performed in a subset of ~80 families.

Results

Three previously reported mutations (IVS1+2-3insT, L513P and A538T) and two novel missense substitutions (C388Y and G515S) were identified in 12 families (i.e. ~8% of non-related Polish PCD patients). The structure of background SNP haplotypes indicated common origin of each of the two most frequent mutations, IVS1+2-3insT and A538T. MLPA analysis did not reveal any significant differences between patients and control samples. The Polish cohort was compared with all the previously studied PCD groups (a total of 487 families): IVS1+2-3insT remained the most prevalent pathogenetic change in DNAI1 (54% of the mutations identified worldwide), and the increased global prevalence of A538T (14%) was due to the contribution of the Polish cohort.

Conclusions

The worldwide involvement of DNAI1 mutations in PCD pathogenesis in families not preselected for ODA defects ranges from 7 to 10%; this global estimate as well as the mutation profile differs in specific populations. Analysis of the background SNP haplotypes suggests that the increased frequency of chromosomes carrying A538T mutations in Polish patients may reflects local (Polish or Slavic) founder effect. Results of the MLPA analysis indicate that no large exonic deletions are involved in PCD pathogenesis.     

Testing for population subdivision and association in four case-control studies

Population structure has been presumed to cause many of the unreplicated disease-marker associations reported in the literature, yet few actual case-control studies have been evaluated for the presence of structure. Here, we examine four moderate case-control samples, comprising 3,472 individuals, to determine if detectable population subdivision is present. The four population samples include: 500 U.S. whites and 236 African Americans with hypertension; and 500 U.S. whites and 500 Polish whites with type 2 diabetes, all with matched control subjects. Both diabetes populations were typed for the PPARg Pro12Ala polymorphism, to replicate this well-supported association (Altshuler et al. 2000). In each of the four samples, we tested for structure, using the sum of the case-control allele frequency chi(2) statistics for 9 STR and 35 SNP markers (Pritchard and Rosenberg 1999). We found weak evidence for population structure in the African American sample only, but further refinement of the sample, to include only individuals with U.S.-born parents and grandparents, eliminated the stratification. Our examples provide insight into the factors affecting the replication of association studies and suggest that carefully matched, moderate-sized case-control samples in cosmopolitan U.S. and European populations are unlikely to contain levels of structure that would result in significantly inflated numbers of false-positive associations. We explore the role that extreme differences in power among studies, due to sample size and risk-allele frequency differences, may play in the replication problem.     

Genetic variation in the serotonin transporter modulates neural system-wide response to fearful faces

A distributed, serotonergically innervated neural system comprising extrastriate cortex, amygdala and ventral prefrontal cortex is critical for identification of socially relevant emotive stimuli. The extent to which a genetic variation of serotonin transporter gene 5-HTTLPR impacts functional connectivity between the amygdala and the other components of this neural system remains little examined. In our study, neural activity was measured using event-related functional magnetic resonance imaging in 29 right-handed, white Caucasian healthy subjects as they viewed mild or prototypical fearful and neutral facial expressions. 5-HTTLPR genotype was classified as homozygous for the short allele ( S/S ), homozygous for the long allele ( L/L ) or heterozygous ( S/L ). S/S showed greater activity than L/L within right fusiform gyrus (FG) to prototypically fearful faces. To these fearful faces, S/S more than other genotype subgroups showed significantly greater positive functional connectivity between right amygdala and FG and between right FG and right ventrolateral prefrontal cortex (VLPFC). There was a positive association between measure of psychoticism and degree of functional connectivity between right FG and right VLPFC in response to prototypically fearful faces. Our data are the first to show that genotypic variation in 5-HTTLPR modulates both the amplitude within and the functional connectivity between different components of the visual object-processing neural system to emotionally salient stimuli. These effects may underlie the vulnerability to mood and anxiety disorders potentially triggered by socially salient, emotional cues in individuals with the S allele of 5-HTTLPR.     

S-related protein can be recombined with self-compatibility in interspecific derivatives ofLycopersicon

Stylar proteins involved in the self-incompatible (SI) response ofLycopersicon hirsutum have been identified and mapped to the locus that controls SI (S locus).L. esculentum, a self-compatible (SC) species of cultivated tomato, does not display these proteins. Hybrids between SCL. esculentum and SIL. hirsutum are self-sterile despite these individuals bearing pollen containing theS allele ofL. esculentum. In progeny derived from backcrossing the hybrids toL. esculentum, there was a strong correlation between the presence of theS allele fromL. hirsutum and self-infertility. However, this relationship was uncoupled in a number of backcross (BC) progeny. The SI response appeared to be nonexistent in two self-fertile BC individuals that were heterozygous for theS allele ofL. hirsutum, based on Mendelian segregation of a tightly linked DNA marker,CD15, in selfed progeny. Among these progeny self-fertile individuals that were homozygous for theL. hirsutum allele of the linked marker were also determined to be homozygous for anS-related protein ofL. hirsutum through test crosses withL. esculentum. Therefore, plants were produced that were homozygous for a functionalS allele but were self-fertile. This result and other evidence suggest that theS-related proteins are not sufficient to elicit a self-incompatible response inL. esculentum and that there is a mutation(s) inL. esculentum somewhere other than theS locus that leads to self-compatibility.     

Strict conservation of the ITS regions of the ribosomal RNA genes in Atlantic cod (Gadus morhua L.).

The nucleotide sequence of the internal transcribed region (ITS) of ribosomal RNA genes from Atlantic cod (Gadus morhua L.) was determined. The complete ITS region spanned approximately 1113 base pairs. The ITS1 region comprised 532 base pairs, the 5.8S region 159, and the ITS2 region contained 422 base pairs. Sequence data were obtained from a total of 12 samples, one pool from six cod and 11 individuals. The sequencing was carried out in two separate experimental periods employing slightly different methodology. The samples were from two different cod stocks, Norwegian costal cod and North East Arctic cod. The sequence analysis showed that in the 12 samples, the ITS region, including the 5.8S RNA, was identical. The ITS region is thus totally conserved in these two cod stocks. The extreme conservation of the ITS regions in the cod rDNA could reflect the small genome size of cod and/or indicate a specific critical role in the processing of the ribosomal units in cold-adapted species.     

Distribution of the HIV resistance CCR5-Delta32 allele among Egyptians and Syrians

A mutant allele of the beta-chemokine receptor gene CCR5 bearing a 32-basepair (bp) deletion that prevents cell invasion by the primary transmitting strain of HIV-1 has recently been characterized. Individuals homozygous for the mutation are resistant to infection, even after repeated high-risk exposure, but this resistance appears not absolute, as isolated cases of HIV-positive deletion homozygotes are emerging. The consequence of the heterozygous state is not clear, but it may delay the progression to AIDS in infected individuals. In order to evaluate the frequency distribution of CCR5-Delta32 polymorphism among Egyptians, a total of 200 individuals (154 from Ismailia and 46 from Sinai) were tested. Only two heterozygous individuals from Ismailia carried the CCR5-Delta32 allele (0.6%), and no homozygous (Delta32/Delta32) individuals were detected among the tested samples. The presence of the CCR5-Delta32 allele among Egyptians may be attributed to the admixture with people of European descent. Thus we conclude that the protective deletion CCR5-Delta32 is largely absent in the Egyptian population.     

De novo Ser72Leu mutation in the peripheral myelin protein 22 in two Polish patients with a severe form of Charcot-Marie-Tooth disease

To date, 12 cases of heterozygous Ser72Leu mutations in the peripheral myelin protein 22 have been reported in patients suffering from severe demyelinating form of Charcot-Marie-Tooth disease (CMT1) and congenital hypomyelinating neuropathy (CHN) [MIM# 605253]. In the present study we report two cases of de novo S72L mutations in the PMP22 gene detected in patients of Polish origin suffering from CMT1 disease.     

Short allele of serotonin transporter gene promoter is a risk factor for obesity in adolescents

Obesity and hypertension are increasing medical problems in adolescents. Serotonin transporter (5-HTT) is involved in mood and eating disturbances. Encoded by the gene SLC6A4, the promoter shows functional insertion/deletion alleles: long (L) and short (S). Because individuals who are carriers for the short version are known to be at risk for higher levels of anxiety, we hypothesized that this variant may be associated with overweight. Data and blood samples were collected from 172 adolescents out of a cross-sectional, population-based study of 934 high school students. To replicate the findings, we also included 119 outpatients from the Nutrition and Diabetes Section of the Children's County Hospital. We found that the S allele was associated with overweight (BMI > 85th percentile), being a risk factor for overweight independently of sex, age, and hypertension [odds ratio (OR): 1.85; 95% confidence interval (CI): 1.13, 3.05; p < 0.02]. Additionally, in the outpatient study, compared with the homozygous LL subjects, S allele carriers showed a higher BMI z-score (1.47 +/- 1.09 vs. 0.51 +/- 1.4; p < 0.002) and were more frequent in overweight children. In conclusion, the S allele of the SLC6A4 promoter variant is associated with overweight being an independent genetic risk factor for obesity.     

Development of a sequence characteristic amplified region marker linked to the L4 locus conferring broad spectrum resistance to tobamoviruses in pepper plants

To develop molecular markers linked to the L4 locus conferring resistance to tobamovirus pathotypes in pepper plants, we performed AFLP with 512 primer combinations for susceptible (S pool) and resistant (R pool) DNA bulks against pathotype 1.2 of pepper mild mottle virus. Each bulk was made by pooling the DNA of five homozygous individuals from a T10 population, which was a near-isogenic BC4F2 generation for the L4 locus. A total of 19 primer pairs produced scorable bands in the R pool. Further screening with these primer pairs was done on DNA bulks from T102, a BC10F2 derived from T10 by back crossing. Three AFLP markers were finally selected and designated L4-a, L4-b and L4-c. L4-a and L4-c each underwent one recombination event, whereas no recombination for L4-b was seen in 20 individuals of each DNA bulk. Linkage analysis of these markers in 112 F2 T102 individuals showed that they were each within 2.5 cM of the L4 locus. L4-b was successfully converted into a simple 340-bp SCAR marker, designated L4SC340, which mapped 1.8 cM from the L4 locus in T102 and 0.9 cM in another BC10F2 population, T101. We believe that this newly characterized marker will improve selection of tobamovirus resistance in pepper plants by reducing breeding cost and time.     

Multivariate characterization of morphological traits in Burkina Faso sheep

A total of 6440 female sheep from Burkina Faso were scored for seven body measurements and four qualitative morphological traits. Sampling included the three main environmental areas and sheep breeds of Burkina Faso: the Sahel area (Burkina-Sahel sheep), the Sudan-Sahel area (Mossi sheep) and the Sudan area (Djallonké sheep). Canonical analyses showed that differences in body measurements between the Sudan and the Sudan-Sahel sheep were small even though most body traits showed higher average values in the Burkina-Sahel sheep: the shortest Mahalanobis distance was found between the Sudan and the Sudan-Sahel populations (1.54), whilst that between the Sudan and the Sahelian populations was the largest (7.88). Discriminant analysis showed that most Sudan (Djallonké) individuals (60.85%) were classified as Sudan-Sahel (Mossi) individuals whilst most Burkina-Sahel individuals were classified into their environmental area of sampling (89.46%). Correspondence analyses indicated that the Burkina-Sahel sheep population clustered together with dropping ears, black and brown colour patterns and presence of wattles, the Sudan sheep were closely associated with long hair and vertical and curled ears and that the Sudan-Sahel sheep did not have clear associations with qualitative phenotypic traits. At the morphological level, the Sudan-Sahel (Mossi) sheep population can be considered a geographical subpopulation belonging to the Djallonké breed, showing some particularities, namely larger body size, due to the particular environmental condition of the area in which it is managed and a continuous gene flow from Sahelian sheep, The information reported in this study will be the basis for the establishment of further characterization, conservation and selection strategies for Burkina Faso sheep.     

Multivariate characterization of morphological traits in Burkina Faso sheep

A total of 6440 female sheep from Burkina Faso were scored for seven body measurements and four qualitative morphological traits. Sampling included the three main environmental areas and sheep breeds of Burkina Faso: the Sahel area (Burkina-Sahel sheep), the Sudan-Sahel area (Mossi sheep) and the Sudan area (Djallonké sheep). Canonical analyses showed that differences in body measurements between the Sudan and the Sudan-Sahel sheep were small even though most body traits showed higher average values in the Burkina-Sahel sheep: the shortest Mahalanobis distance was found between the Sudan and the Sudan-Sahel populations (1.54), whilst that between the Sudan and the Sahelian populations was the largest (7.88). Discriminant analysis showed that most Sudan (Djallonké) individuals (60.85%) were classified as Sudan-Sahel (Mossi) individuals whilst most Burkina-Sahel individuals were classified into their environmental area of sampling (89.46%). Correspondence analyses indicated that the Burkina-Sahel sheep population clustered together with dropping ears, black and brown colour patterns and presence of wattles, the Sudan sheep were closely associated with long hair and vertical and curled ears and that the Sudan-Sahel sheep did not have clear associations with qualitative phenotypic traits. At the morphological level, the Sudan-Sahel (Mossi) sheep population can be considered a geographical subpopulation belonging to the Djallonké breed, showing some particularities, namely larger body size, due to the particular environmental condition of the area in which it is managed and a continuous gene flow from Sahelian sheep, The information reported in this study will be the basis for the establishment of further characterization, conservation and selection strategies for Burkina Faso sheep.