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PubMed1992

Evaluation of the PhP system for biochemical-fingerprint typing of strains of Salmonella of serotype Typhimurium.

The Phene Plate (PhP) system of biochemical fingerprinting of bacteria is a computerised typing system, based on quantitative measurements of the kinetics of several biochemical reactions of bacteria grown in liquid medium in microtitration plates. For each isolate tested, it yields a biochemical fingerprint comprising several kinds of quantitative data which are useful for establishing similarities among strains with a personal-computer program. In this study, a set of 16 specific substrates was chosen to differentiate strains of Salmonella of serotype Typhimurium. The system was evaluated for its typability, reproducibility and discriminatory power in tests with a collection of 100 epidemiologically unrelated Typhimurium strains and results were compared with those obtained by phage typing. At an identity level of 0.980, strains were assigned by this method to 51 biochemical phenotypes (BPTs), giving a diversity index of 0.963 and a resolution index of 0.210. In contrast, 24 phage types (PTs) were identified among these isolates (a diversity index of 0.901). The combined use of biochemical fingerprinting by the PhP system and phage typing discriminated 82 phenotypes (a diversity index of 0.994). Stability of markers in each of the methods was also evaluated after subculture of 20 strains for 21 consecutive days. Only nine biochemical reactions were found that were subject to small, but measurable, changes for at least one isolate. These changes slightly decreased the mean similarity coefficients among strains but the overall BPTs of the strains showed changes in four strains (20%). In contrast, eight strains (40%) showed changes in their PTs after this treatment. It is concluded that the PhP system is a highly discriminatory and reproducible method for typing Typhimurium strains. It is easy to perform, and may be used alone or in combination with phage typing in epidemiological studies of Typhimurium strains.

Bacterial Typing Techniques↗

PubMed1996

Qualitative and quantitative contributions of the T cell receptor zeta chain to mature T cell apoptosis.

Engagement of the T cell receptor (TCR) of mature T lymphocytes can lead either to activation/proliferation responses or programmed cell death. To understand the molecular regulation of these two fundamentally different outcomes of TCR signaling, we investigated the participation of various components of the TCR-CD3 complex. We found that the TCR-zeta chain, while not absolutely required, was especially effective at promoting mature T cell apoptosis compared with the CD3 epsilon, gamma, or delta chains. We also carried out mutagenesis to address the role of the immunoreceptor tyrosine-based activation motifs (ITAMs) that are the principal signaling components found three times in the TCR-zeta chain and once in each of the CD3 epsilon, gamma, or delta chains. We found that the ability of the TCR-zeta chain to promote apoptosis results both from a quantitative effect of the presence of multiple ITAMs as well as qualitatively different contributions made by individual ITAMs. Apoptosis induced by single chain chimeras revealed that the first zeta ITAM stimulated greater apoptosis than the third zeta ITAM, and the second zeta ITAM was unable to trigger apoptosis. Because microheterogeneity in the amino acid sequence of the various ITAM motifs found in the TCR-zeta and CD3 chains predicts interactions with distinct src-homology-2-domain signaling proteins, our results suggest the possibility that individual ITAM motifs might play unique roles in TCR responses by engaging specific signaling pathways.

Amino Acid Sequence↗

PubMed2005

Divergence between motoneurons: gene expression profiling provides a molecular characterization of functionally discrete somatic and autonomic motoneurons.

Studies in the developing spinal cord suggest that different motoneuron (MN) cell types express very different genetic programs, but the degree to which adult programs differ is unknown. To compare genetic programs between adult MN columnar cell types, we used laser capture microdissection (LCM) and Affymetrix microarrays to create expression profiles for three columnar cell types: lateral and medial MNs from lumbar segments and sympathetic preganglionic motoneurons located in the thoracic intermediolateral nucleus. A comparison of the three expression profiles indicated that approximately 7% (813/11,552) of the genes showed significant differences in their expression levels. The largest differences were observed between sympathetic preganglionic MNs and the lateral motor column, with 6% (706/11,552) of the genes being differentially expressed. Significant differences in expression were observed for 1.8% (207/11,552) of the genes when comparing sympathetic preganglionic MNs with the medial motor column. Lateral and medial MNs showed the least divergence, with 1.3% (150/11,552) of the genes being differentially expressed. These data indicate that the amount of divergence in expression profiles between identified columnar MNs does not strictly correlate with divergence of function as defined by innervation patterns (somatic/muscle vs. autonomic/viscera). Classification of the differentially expressed genes with regard to function showed that they underpin all fundamental cell systems and processes, although most differentially expressed genes encode proteins involved in signal transduction. Mining the expression profiles to examine transcription factors essential for MN development suggested that many of the same transcription factors participate in combinatorial codes in embryonic and adult neurons, but patterns of expression change significantly.

Animals↗

PubMed1996

Nasopharyngeal cancer in a low-risk population: defining risk factors by histological type.

Nasopharyngeal cancer (NPC) is a major public health problem in parts of Southeast Asia and North Africa, but is rare among whites and blacks. Although infection with the EBV and genetic susceptibility appear to play large roles in high-incidence populations, migrant studies suggest that environmental factors may also be important. Aside from the high risks associated with ingestion of salted fish, surprisingly few other risk factors have been established from studies in endemic areas. We studied a low-incidence population to determine whether tobacco use, alcohol consumption, and certain medical conditions and treatments are related to NPC and to examine variations in risk by histology. We reasoned that new relationships might be best identified in the absence of strong causal pathways, such as intake of preserved foods and genetic susceptibility. A population-based case-control study was conducted from 1987 to 1993 at five cancer registries in the United States: western Washington, metropolitan Detroit, Connecticut, Iowa, and Utah. Controls were identified by random digit dialing and frequency matched to the gender and age distribution of cases at each registry. Telephone interviews were completed by 231 cases and 246 controls. We observed a strong dose-response relationship between cigarette smoking and risk of differentiated squamous cell carcinoma (test for trend, P < .001). The highest risk [odds ratio (OR), 6.5; 95% confidence interval (CI), 2.0-21.3] occurred among current smokers with a history of more than 60 pack-years. In contrast, there was no evidence that undifferentiated or nonkeratinizing carcinomas were associated with cigarette smoking. Similarly, a significant increase in risk was observed for the heaviest alcohol consumers (21 or more drinks/week) only for differentiated squamous cell carcinomas (OR, 2.9; 95% CI, 1.2-6.9). The associations with cigarettes and alcohol appeared to be stronger among persons 50 years or older. There was a suggestion that diagnosis with infectious mononucleosis (a marker of late infection with EBV) is linked with decreased NPC risk (OR, 0.4; 95% CI, 0.1-1.1). This report indicates that over two-thirds of differentiated squamous cell NPC cases arising in older persons in the United States can be accounted for by cigarettes and alcohol, but leaves unexplained cases arising in the young and carcinomas of undifferentiated or nonkeratinizing histology. Future studies of NPC need to take into account histology and age in evaluating these and other environmental and genetic risk factors.

Adult↗

PubMed1994

Therapy-related acute myeloid leukemia following treatment with epipodophyllotoxins: estimating the risks.

In the past decade, therapy-related acute myeloid leukemia (t-AML) following treatment with regimens that include inhibitors of topoisomerase-II (TOPO-II) has been reported with increasing frequency. These cases of t-AML generally have a shorter latency period than t-AML following alkylator therapy, are associated with chromosomal translocations (especially involving chromosome band 11q23), and usually present as M4 or M5 FAB subtype. Although the epipodophyllotoxins (etoposide and teniposide) have been most often implicated, similar cases of t-AML occur following therapy with other classes of Topo-II inhibitors (e.g., anthracyclines). There is wide variation in published studies in the estimates of risk of t-AML following epipodophyllotoxin therapy. These varying estimates may reflect a number of factors, including: small sample size leading to large confidence intervals around risk estimates; varying susceptibility of different patient populations; varying schedules of epipodophyllotoxin administration; different cumulative doses of epipodophyllotoxins; and administration of epopodophyllotoxins with additional agents that may alter the leukemogenic effect of the epipodophyllotoxins. Available data suggest that children with acute lymphocytic leukemia (ALL) treated with high cumulative doses of epipodophyllotoxins using either weekly or twice-weekly schedules of administration have a relatively high risk of developing t-AML (5-12% cumulative risk). On the other hand, germ cell patients treated with relatively low cumulative doses of etoposide (usually 1,500-2,500 mg/m2) appear to have a low risk for developing t-AML. There is inadequate experience at this time with higher cumulative doses of etoposide (e.g., 4,000-5,000 mg/m2 as used for pediatric solid tumors) given on a daily x 5 schedule to allow estimates of risk to be developed for this schedule and cumulative dose. The Cancer Therapy Evaluation Program (CTEP) of the National Cancer Institute (NCI) has developed a monitoring plan designed to obtain reliable estimates of the risk of t-AML following epipodophyllotoxin treatment. Twelve Cooperative Group clinical trials that use epipodophyllotoxins at either low (< 1,500 mg/m2), moderate (1,500-3,999 mg/m2), or higher cumulative doses (> 4,000 mg/m2) are being prospectively monitored for cases of t-AML occurring among patients entered onto the trials.

Alkylating Agents↗

PubMed1997

Molecular epidemiology of rabies epizootics in Texas.

BACKGROUND: Texas is in the midst of two independent epizootics of rabies, involving coyotes (Canis latrans) and domestic dogs (Canis familiaris) in southern Texas and grey foxes (Urocyon cinereoargenteus) in west central Texas. The domestic dog/coyote (DDC) and grey for (TF) rabies virus variants cannot be differentiated by antigenic typing with currently available monoclonal antibodies. These two variants also cannot be distinguished from a third variant, Sonora dog (SD) rabies, that is not enzootic in Texas, but occasionally occurs in animals along the western border with Mexico. OBJECTIVES: To determine a method for the differentiation of the DDC. TF and SD variants, which is essential for epidemiologic monitoring of the Oral Rabies Vaccination Program (ORVP), a program instituted to control rabies in coyotes and grey foxes in Texas. STUDY DESIGN: Primers complementary to nucleoprotein sequence of either the DDC or TF rabies virus permit specific reverse transcription and amplification by polymerase chain reaction. In addition, general primers, which recognize a broad range of rabies variants, used in conjunction with a restriction digest for the differentiation of DDC, TF of SD rabies virus were investigated. RESULTS AND CONCLUSIONS: Of 122 specimens tested with specific primers. 111 (91%) were specifically identified as either DDC (33 samples) or TF (78 samples). Overly stringent conditions, enzyme inhibitors, or limiting RNA may account for the 11 non-amplifications. Amplification of RNA under less stringent conditions, with primers recognizing a broad range of rabies variants followed by digestion with either restriction enzyme Desulfovibrio desulfuricans I (Dde I) or Haemophilus influenzae Rf. (HinfI), was used to identify the 11 isolates that did not amplify with specific primers (6 DDC, 4 TF and 1 SD). In addition to these 11 isolates, the less stringent method of amplification, followed by enzyme digestion has identified a total of 125 additional specimens (26 DDC, 94 TF and 5 SD) that were not tested by variant-specific amplification. These data provide a means to track the spread of the different rabies virus variants and allow the ORVP to plan its vaccine disbursement by defining the two epizootic boundaries.

Animals↗

PubMed1999

Changes of hepatitis B surface antigen variants in carrier children before and after universal vaccination in Taiwan.

Mutants of a determinant of hepatitis B surface antigen (HBsAg) identified in vaccinated children pose a potential threat to long-term success of vaccination programs. We examined the mutants of a determinant (residues 110-160) of HBsAg in hepatitis B virus (HBV) DNA-positive children identified during previous serosurveys in Taipei undertaken just before (1984), 5 years after (1989), and 10 years after (1994) universal vaccination began. In HBV DNA-positive children from 3 surveys, the prevalence of a determinant mutants increased from 8 of 103 (7.8%) in 1984 to 10 of 51(19.6%) in 1989 and 9 of 32 (28.1%) in 1994 and was higher in those fully-vaccinated than unvaccinated (12/33 vs. 15/153, P =. 0003). Most amino acid changes of the variants clustered in residues 125-129 and 140-149. In all 27 children with detectable mutants, the mean age of those vaccinated was younger than those unvaccinated (4. 8 +/- 3.8 vs. 7.9 +/- 2.3 yrs, P <.05); and mutations occurred in a region with greatest local hydrophilicity (residues 140-149) more frequently in those vaccinated than in those unvaccinated (10/12 vs. 6/15, P =.0253). More mutated residues and more mutations at neutralizing epitopes, such as N146, C147, T148, and C149, were found in the 1994 survey. Vaccinated children may contract variant infections through vertical or horizontal transmission. Universal vaccination has accelerated an accumulation of HBsAg a determinant mutants with amino acid changes critical for immune escape in vaccinated children who became carriers, suggesting that new vaccination strategies should be considered.

Carrier State↗

PubMed1997

Muscle-specific creatine kinase gene polymorphism and VO2max in the HERITAGE Family Study.

This study examined the association between a DNA polymorphism in the muscle-specific creatine kinase (CKMM) gene and VO2max in the sedentary state, as well as its response (deltaVO2max) to a standardized 20-wk endurance training program. The subjects were 160 biologically unrelated Caucasian parents (80 women, 80 men) and 80 biologically unrelated adult offspring of the HERITAGE Family Study. The CKMM polymorphism was detected by PCR and digestion with the NcoI restriction enzyme. VO2max was measured during maximal cycle ergometer tests. VO2max was 2119 +/- 45 mL x min(-1) (mean +/- SE) or 26 +/- 0.4 mL x kg(-1) x min(-1). Both sexes had a significant (P < 0.05) increase in the deltaVO2max (women = 283 +/- 20 mL x min[-1] and men = 363 +/- 25 mL x min[-1]). Allele and genotype frequencies were not significantly different (P > 0.05) between sexes. Age and sex adjusted VO2max was significantly (P = 0.007) associated with the CKMM genotype in the parents, whereas no association (P > 0.05) was observed in the offspring. DeltaVO2max values adjusted for age, sex, VO2max, and body mass were characterized by genotype differences in both parents (P = 0.0004) and offspring (P = 0.0025). A significantly (P < 0.05) lower deltaVO2max to endurance training was detected in both parents and offspring homozygotes for the rare allele. The genotype accounted for at least 9% of the variance in deltaVO2max. These results indicate that the NcoI polymorphism in the 3' untranslated region of the muscle-specific creatine kinase gene is associated with the deltaVO2max to endurance training.

Adult↗

PubMed2000

Varicella-zoster virus gE escape mutant VZV-MSP exhibits an accelerated cell-to-cell spread phenotype in both infected cell cultures and SCID-hu mice.

Varicella-zoster virus is considered to have one of the most stable genomes of all human herpesviruses. In 1998, we reported the unanticipated discovery of a wild-type virus that had lost an immunodominant B-cell epitope on the gE ectodomain (VZV-MSP); the gE escape mutant virus exhibited an unusual pattern of egress. Further studies have now documented a markedly enhanced cell-to-cell spread by the mutant virus in cell culture. This property was investigated by laser scanning confocal microscopy combined with a software program that allows the measurement of pixel intensity of the fluorescent signal. For this new application of imaging technology, the VZV immediate early protein 62 (IE 62) was selected as the fluoresceinated marker. By 48 h postinfection, the number of IE 62-positive pixels in the VZV-MSP-infected culture was nearly fourfold greater than the number of pixels in a culture infected with a low-passage laboratory strain. Titrations by infectious center assays supported the above image analysis data. Confirmatory studies in the SCID-hu mouse documented that VZV-MSP spread more rapidly than other VZV strains in human fetal skin implants. Generally, the cytopathology and vesicle formation produced by other strains at 21 days postinfection were demonstrable with VZV-MSP at 14 days. To assess whether additional genes were contributing to the unusual VZV-MSP phenotype, approximately 20 kb of the VZV-MSP genome was sequenced, including ORFs 31 (gB), 37 (gH), 47, 60 (gL), 61, 62 (IE 62), 66, 67 (gI), and 68 (gE). Except for a few polymorphisms, as well as the previously discovered mutation within gE, the nucleotide sequences within most open reading frames were identical to the prototype VZV-Dumas strain. In short, VZV-MSP represents a novel variant virus with a distinguishable phenotype demonstrable in both infected cell cultures and SCID-hu mice.

Animals↗

PubMedDate not supplied

Methodological issues in setting up a surveillance system for birth defects in India.

India is undergoing an epidemiological transition--communicable diseases are on the decline due to better living conditions and healthcare delivery. On the other hand, the relative increase in the prevalence of non-communicable, chronic and genetic diseases threatens to be a public health problem in India. One such group of disorders is congenital malformations. Though several studies have been done on congenital malformations in India since the early 1960s, coinciding with the thalidomide tragedy in the West, no uniform methods are available for the surveillance of birth defects. Each study has come out with varying results, not only because of the geographic variation in birth defects but also due to the varying standards adopted by each study in data collection, case definition and other methodological issues. Setting up a mechanism to understand the extent and nature of birth defects would involve the creation of a birth defects registry. The goals and objectives of such a registry should be formulated before it is set up. There are three types of registries-descriptive, analytical and preventive. These can also be classified as population- or hospital-based. Whether a registry is population- or hospital-based depends largely on the movement of mothers for delivery, registration of vital events in an area defined by the programme, as well as the resources available to the registry. Data can be collected in a passive or active manner, which also depends on the resources available to the registry. Every registry should have its own working definition of eligible cases to be reported, depending on the diagnostic services available in that area, and multiple sources of information should be used to improve the ascertainment rate. All the diagnostic terms should be coded and the information collected should be stored in a well-constructed database, preferably a relational type. Registries must evaluate their methods of data collection periodically to estimate the number of false-positive and false-negative reports. Ethical issues, cost and funding for the employment of various specialized professionals should be considered before setting up a registry.

Congenital Abnormalities↗

PubMed2005

Practical significance of heterogeneity among BVDV strains: impact of biotype and genotype on U.S. control programs.

In the early 1990s research groups in North America noted that a newly recognized severe acute form of bovine viral diarrhea virus infection, referred to as hemorrhagic syndrome or severe acute BVDV (SA BVDV), was associated with a genetically distinct subgroup of BVDV strains. This new subgroup was named BVDV genotype 2 or BVDV2. All BVDV strains previously characterized in the literature belonged to a separate genotype, BVDV1. However, not all strains identified as BVDV2 were associated with severe acute infections. If I did this deletion, I did not mean to do it. I think it was already here, though. I see there are some other big edits that I did not do; fine. Hollis subsequent surveys of BVDV strains isolated from clinical submissions to diagnostic laboratories and contaminated fetal calf serum suggested that the ratio of BVDV2 to BVDV1 strains in the U.S. approached 50%. Further, while antigenic cross reactivity is seen between BVDV1 and BVDV2 strains, a log or more difference is typically observed in titers against viruses from different genotypes. These observations prompted vaccine manufacturers in North America to produce vaccines against BVDV that contained antigens from both BVDV1 and BVDV2 strains. Under experimental conditions, these new vaccines offered improved protection against type 2 strains, however field data are still insufficient to assess their efficacy in practice. The BVDV genotypes may also be segregated into subgenotypes. Two subgenotypes of both BVDV1 (BVDV1a and BVDV1b) and BVDV2 (BVDV2a and BVDV2b) have been reported in North American. BVDV2a predominates with BVDV2b isolation a rare event. In contrast, BVDV1a and BVDV1b are both commonly isolated. Antigenic differences observed between strains from the BVDV1a and BVDV1b subgenotypes have led to the suggestion that protection may be improved by inclusion of strains from both BVDV1a and BVDV1b in vaccines in addition to BVDV2. The cost to benefit ratio of this proposal is currently a matter of debate.

Animals↗

PubMed2006

Reconsidering the human immunoglobulin heavy-chain locus: 1. An evaluation of the expressed human IGHD gene repertoire.

We have used a bioinformatics approach to evaluate the completeness and functionality of the reported human immunoglobulin heavy-chain IGHD gene repertoire. Using the hidden Markov-model-based iHMMune-align program, 1,080 relatively unmutated heavy-chain sequences were aligned against the reported repertoire. These alignments were compared with alignments to 1,639 more highly mutated sequences. Comparisons of the frequencies of gene utilization in the two databases, and analysis of features of aligned IGHD gene segments, including their length, the frequency with which they appear to mutate, and the frequency with which specific mutations were seen, were used to determine the reliability of alignments to the less commonly seen IGHD genes. Analysis demonstrates that IGHD4-23 and IGHD5-24, which have been reported to be open reading frames of uncertain functionality, are represented in the expressed gene repertoire; however, the functionality of IGHD6-25 must be questioned. Sequence similarities make the unequivocal identification of members of the IGHD1 gene family problematic, although all genes except IGHD1-14*01 appear to be functional. On the other hand, reported allelic variants of IGHD2-2 and of the IGHD3 gene family appear to be nonfunctional, very rare, or nonexistent. Analysis also suggests that the reported repertoire is relatively complete, although one new putative polymorphism (IGHD3-10*p03) was identified. This study therefore confirms a surprising lack of diversity in the available IGHD gene repertoire, and restriction of the germline sequence databases to the functional set described here will substantially improve the accuracy of IGHD gene alignments and therefore the accuracy of analysis of the V-D-J junction.

Alleles↗

PubMed1997

Molecular characterization of two Bordetella bronchiseptica strains isolated from children with coughs.

During a surveillance program associated with the Italian clinical trial for the evaluation of new acellular pertussis vaccines, two bacterial isolates were obtained in cultures of samples from immunocompetent infants who had episodes of cough. Both clinical isolates were identified as Bordetella bronchiseptica by biochemical criteria, although both strains agglutinated with antisera specific for Bordetella parapertussis, suggesting that the strains exhibited some characteristics of both B. bronchiseptica and B. parapertussis. Both children from whom these strains were isolated exhibited an increase in serum antibody titer to pertussis toxin (PT), a protein that is produced by Bordetella pertussis but that is not thought to be produced by B. bronchiseptica. We therefore examined whether the clinical isolates were capable of producing PT. Neither strain produced PT under laboratory conditions, although both strains appeared to contain a portion of the ptx region that encodes the structural subunits of PT. In order to determine whether the ptx genes may encode functional proteins, we inserted an active promoter directly upstream of the ptx region of one of these strains. Biologically active PT was produced, suggesting that this strain contains the genetic information necessary to encode an active PT molecule. Sequence analysis of the ptx promoter region of both strains indicated that, while they shared homology with the B. bronchiseptica ATCC 4617 sequence, they contained certain sequence motifs that are characteristic of B. parapertussis and certain motifs that are characteristic of B. pertussis. Taken together, these findings suggest that variant strains of B. bronchiseptica exist and might be capable of causing significant illness in humans.

Acute Disease↗

PubMed2026

Genotype-Guided Antidepressant Prescribing for Patients With Depression: A Randomized Clinical Trial.

IMPORTANCE: The effectiveness of pharmacogenetics to guide prescribing of selective serotonin reuptake inhibitors (SSRIs) for depression remains unclear, despite the well-established association between SSRI pharmacokinetics and genetic variation. OBJECTIVE: To determine whether pharmacogenetic-guided prescribing of SSRIs improves treatment response in patients with depression. DESIGN, SETTING, AND PARTICIPANTS: The ADOPT PGx (A Depression and Opioid Pragmatic Trial in Pharmacogenetics) Depression pragmatic randomized clinical trial was conducted from August 10, 2021, through April 27, 2024, at primary care, psychiatry, or family medicine clinics at enrolling sites throughout the US. Patients were aged 8 years or older and had experienced depression for 3 months or longer. INTERVENTION: Patients were randomized to genotype-guided SSRI prescribing (intervention group) or usual care (control group). Actionable drug metabolism phenotypes were defined as those for which pharmacogenetic clinical guidelines recommend alternative medication selection or dose adjustment. MAIN OUTCOMES AND MEASURES: The primary outcome was change in Patient-Reported Outcomes Measurement Information System (PROMIS) depression T scores at 3 months among patients with the actionable phenotype. Secondary end points included adverse effect severity of SSRIs at 3 months and depression remission (measured with PROMIS depression scores and Patient Health Questionnaire-8 [PHQ-8] scores) at 6 months. RESULTS: This study of 1460 patients included 1239 adults (84.9%) (mean [SD] age, 40.6 [16.7] years) and 221 children (15.1%) (mean [SD] age, 14.6 [1.8] years). Most patients were female (1096 [75.1%]). A total of 692 patients (47.4%) had an actionable phenotype; 351 (50.7%) were assigned to the intervention, and 341 (49.3%) were assigned to usual care. At baseline, 463 of the 692 patients (66.9%) reported having depressive symptoms for more than 2 years, 603 (87.1%) were receiving pharmacologic treatment, and 354 (51.2%) were receiving nonpharmacologic treatment. At 3 months, no significant differences were observed between the intervention and usual care groups in change in PROMIS depression T scores (mean [SD] change, -4.3 [8.4] vs -4.0 [8.1]; P = .68), medication adverse effect burden (mean [SD] change, 8.2 [4.3] vs 7.8 [4.5]; P = .37), or Patient Health Questionnaire-8 score change (mean [SD] change, -3.3 [5.2] vs -2.7 [4.8]; P  = .13). However, at 6 months, the PROMIS depression T-score remission rate (score ≤16) was higher in the intervention group compared with the usual care group (153 of 317 patients [48.3%] vs 122 of 310 patients [39.4%]; P = .02). CONCLUSIONS AND RELEVANCE: In this randomized clinical trial, genotype-guided prescribing of SSRIs did not improve control of depression symptoms at 3 months compared with usual care but was associated with higher depression remission rates at 6 months. These findings suggest a possible longer-term clinical benefit and indicate that future studies should focus on the durability and long-term impact of genotype-guided prescribing in the management of depressive symptoms. TRIAL REGISTRATION: ClinicalTrials.gov Identifiers: NCT04445792 (Master Protocol Research Program platform trial) and NCT05966155 (ADOPT PGx Depression trial).

Humans↗

PubMed1996

Skin allograft survival in chicken strains with spontaneous autoimmune diseases.

Skin grafts were performed to prove the level of genetic diversity in chicken populations of the Obese strain (OS), which develops a spontaneous Hashimoto's-like thyroiditis, and University of California at Davis (UCD) Line-200 chickens, which are hereditarily afflicted with progressive systemic sclerosis (scleroderma). As controls, Cornell C-strain (CS) and inbred, normal White Leghorn CB chickens were included in the genetic monitoring program. At the commencement of this study in 1988, median allograft rejections were observed after 9 to 12 d (range 8 to 14 d) in OS and CS chickens that derived from large flocks at Cornell University, whereas OS sublines of the smaller, more closely-bred colonies at the University of Innsbruck, Austria, showed median allograft rejection after 19 d (range 12 to 35 d). From 1988 to 1993, allograft survival was only slightly prolonged in the OS sublines. However, the results of the skin allotransplantations in inbred UCD-200 chickens revealed two subpopulations in this line. In one subgroup the median of allograft rejection was calculated with 13 d (range 6 to 37 d) in 1989, 30 d (10 to 37 d) in 1990, 21 d (8 to 90 d) in 1991, and 16 d (7 to 26 d) in 1993. In the other subgroup allografts were accepted at rates similar to autografts. In addition, the inbreeding coefficient was calculated for eight male and eight female OSB5B5Cornell (C) and OSB5B5Innsbruck (INN) chickens, respectively, hatched in 1993. On the basis of mating records, the minimal estimate of the inbreeding coefficient was calculated to be 0.0679 in the OSB5B5C and 0.1035 in the OSB5B5INN population. The results demonstrated a higher degree of consanguinity in the smaller population of OSB5B5INN chickens compared to OSB5B5C birds. The later are maintained in larger numbers, therefore, the frequency of matings between related individuals should be lower.

Animals↗

PubMed2005

[Variations within OLF1/EBF-associated zinc finger protein gene confer susceptibility to lupus nephritis in Chinese population].

OBJECTIVE: To observe whether single nucleotide polymorphisms (SNPs) within the OLF1/EBF-associated zinc finger protein (OAZ) gene are associated with lupus nephritis (LN) susceptibility in Chinese population. METHODS: Eight SNPs located around the positive microsatellite marker D16S517 within OAZ gene with relatively high heterozygosity were chosen for genotyping on 184 systemic lupus erythromatosus (SLE) patients, including 101 non-LN patients and 83 LN patients, and 286 normal controls using TaqMan MGB allelic discrimination method. Data were collected by SDS 2.0 software. Haplotypes and their frequencies were constructed and estimated, and linkage disequilibrium analysis between pairs of SNPs was evaluated by calculating the D Prime using Helixtree program. Case-control study was performed between the SLE, LN, and non-LN groups and normal control group. RESULTS: (1) The frequency of SNP rs1344531 T allele was 47.0% in the SLE patients, significantly higher than that in the controls [38.1%,; chi(2) = 7.300, P = 0.008, OR (95% CI) = 1.441 (1.105 - 1.878)], which showed that the frequency of SNP rs1344531 T allele is associated with SLE susceptibility. The genotypic distribution of SNP rs1344531(CC/CT/TT) differed significantly between the SLE patients (25.5%/54.9%/19.6%) and normal controls (38.1%/47.6%/14.3%) (chi(2) = 8.394, P = 0.015). The CC genotype frequency of the SLE patients was 25.5%, significantly lower than that of the normal controls [38.1%; chi(2) = 7.976, P = 0.005, OR (95% CI) = 0.557 (0.370 - 0.838)] (2) The SNP rs1344531 T allele frequency of the SLE patients was 53.0%, significantly higher than that of the normal controls [38.1%; chi(2) = 11.769, P = 0.001, OR (95% CI) = 1.832 (1.293 - 2.596)], which showed an associated between SNP rs1344531 T allele frequency and LN susceptibility. The genotypic distribution of SNP rs1344531 (CC/CT/TT) differed significantly between the LN patients (22.9%/48.2%/28.9%) and the normal controls (38.1%/47.6%/14.3%) (chi(2) = 12.065, P = 0.002). The CC genotype frequency of the LN patients was 22.9%, significantly lower than that of the normal controls (38.1%) [chi(2) = 6.578, P = 0.013, OR (95% CI) = 0.481 (0.274 - 0.848)]. The TT genotype frequency of the LN patients was 28.9%, significantly higher than that of the normal controls (14.3%) [chi(2) = 9.423, P = 0.003, OR (95% CI) = 2.431 (1.363 - 4.334)]. No statistical significance was observed between the non-LN patients and normal controls in TT genotype frequency. (3) The frequencies of haplotypes containing rs1344531:rs1420676-rs1344531(C-T) [chi(2) = 11.731, P = 0.001, OR (95% CI) = 1.867 (1.302 - 2.676)], rs3803665-rs1420676-rs1344531(C-C-T) [chi(2) = 8.876, P = 0.004, OR (95% CI) = 1.772 (1.213 - 2.589)], and rs2292155-rs3803665-rs1420676-rs1344531(C-C-C-T) [chi(2) = 9.962, P = 0.002, OR (95% CI) = 1.915 (1.274 - 2.880)] were all significantly higher in the LN patients in comparison with the normal control group (41.0% versus 27.1%; 33.3% versus 21.8%; and 27.0% versus 16.2%); while the frequencies of other haplotypes: rs1344531-rs2080353(C-A) [chi(2) = 8.06, P = 0.005, OR (95% CI) = 0.603 (0.424 - 0.856)], rs1344531-rs2080353-rs933564 (C-A-G) [chi(2) = 7.929, P = 0.006, OR (95% CI) = 0.602 (0.422 - 0.859)] were significantly lower than those of the normal control group (39.5% versus 52.2%, and 36.6% versus 49.2%), which produced additional support for such association. CONCLUSION: SNP rs1344531 and some haplotypes containing SNP rs1344531 within OAZ are significantly associated with LN susceptibility. Genetic variants of the OAZ gene are involved in the pathogenesis of LN.

Adult↗

PubMed2003

Modulation of gene expression by extracellular pH variations in human fibroblasts: a transcriptomic and proteomic study.

Homeostasis of the intracellular ionic concentration, in particular that of hydrogen ions, is pivotal to the maintenance of cell function and viability. Nonetheless, pH fluctuations in both the intracellular and the extracellular compartments can occurr during development, in physiological processes and in disease. The influence of pH variations on gene expression has been studied in different model systems, but only for a limited number of genes. We have performed a broad range analysis of the patterns of gene expression in normal human dermal fibroblasts at two different pH values (in the presence and in the absence of serum), with the aim of getting a deeper insight into the regulation of the transcriptional program as a response to a pH change. Using the Affymetrix gene chip system, we found that the expression of 2068 genes (out of 12 565) was modulated by more than two-fold at 24, 48 or 72 h after the shift of the culture medium pH to a more acidic value, stanniocalcin 1 being a remarkable example of a strongly up-regulated gene. Genes displaying a modulated pattern of expression included, among others, cell cycle regulators (consistent with the observation that acidic pH abolishes the growth of fibroblasts in culture) and relevant extracellular matrix (ECM) components. Extracellular matrix protein 2, a protein with a restricted pattern of expression in adult human tissues, was found to be remarkably overexpressed as a consequence of serum starvation. Since ECM components, whose expression is controlled by pH, have been used as targets for biomolecular intervention, we have complemented the Affymetrix analysis with a two-dimensional polyacrylamide gel electrophoresis analysis of proteins which are differentially secreted by fibroblasts at acidic or basic pH. Mass spectrometric analysis of more than 650 protein spots allowed the identification of 170 protein isoforms or fragments, belonging to 40 different proteins. Some proteins were only expressed at basic pH (including, for instance, tetranectin), while others (e.g., agrin) were only detectable at acidic pH. Some of the identified proteins may represent promising candidate targets for biomedical applications, e.g., for antibody-mediated vascular targeting strategies.

Cells, Cultured↗

PubMed1995

Heterogeneity of variance by sire breed, sex, and dam breed in 200- and 365-day weights of beef cattle from a top cross experiment.

The nature of the heterogeneity of variance for 200- and 365-d weights by sex, sire breed, and dam breed subclasses was studied. Data consisted of records for weaning (n = 7,829) and yearling (n = 7,367) weights of progeny from 673 and 672 sires, respectively, from 22 breeds that have been evaluated in the Germ Plasm Evaluation Program at the U.S. Meat Animal Research Center, Clay Center, NE. Sires were mated to Hereford and Angus cows. Each trait was analyzed separately. Three studies were undertaken separately to investigate heterogeneity due to the different factors (i.e., sire breed, sex, or dam breed). Only data from seven sire breeds were used to study the factor sire breed, but all data (22 sire breeds) were used to study the factors sex and dam breed. In each study, three sire and dam models with records of animals of the four sex x dam breed combinations considered different traits and with the same model equation, but covariance structures for random effects (sires, dams, and residuals) of increasing generality were fitted. First, (co)variances across subclasses were assumed equal. Second, correlations and fractions of phenotypic variance were assumed equal but phenotypic variance differed by sire breed, sex, or dam breed as appropriate. Third, variances and covariances were different for each subclass of the factor under study. Variance components were estimated by derivative-free REML. Models for each trait and each factor were compared through likelihood ratio tests. For both traits, variances differed (P < .02) in scale, but not as fractions of phenotypic variance (P > .10), by sire breed and sex subclasses. Variances were not different (P > .10) by dam breed subclasses, either in scale or as fractions of phenotypic variance. Estimates of correlations among genetic effects on weights of calves from different sex-dam breed subclasses were at least .85. Across all sex, sire breed, and dam breed subclasses, pooled estimates of sire and dam variances as fractions of phenotypic variance were, respectively, .06 and .39 for weaning weight and .11 and .24 for yearling weight. The conclusion is that the assumption of equal phenotypic variances among sire breeds and between sexes may not be appropriate in genetic evaluations.

Algorithms↗