Clinical pharmacist intervention in contraindications of the co-administration of cefoperazone and ambroxol hydrochloride injection.

BACKGROUND: Clinical pharmacists identified contraindications in two cases concerning the co-administration of cefoperazone and ambroxol hydrochloride injection, prompting a thorough investigation. CASE PRESENTATION: Clinically, two cases of contraindications for the co-administration of cefoperazone and ambroxol hydrochloride injection were discovered. After the intervention and analysis by clinical pharmacists, the possible reason could be the precipitation of free alkali due to the immediate administration of ambroxol after the infusion of cefoperazone. Clinical pharmacists suggested avoiding the co-administration of the two and recommended flushing the intravenous lines with 5% glucose injection or 0.9% sodium chloride injection during intravenous infusion to prevent direct drug interaction causing precipitation, thereby reducing the occurrence of adverse events. No adverse events occurred after the intervention, and no harm was caused to the patients. CONCLUSIONS: The co-administration of cefoperazone and ambroxol hydrochloride injection can lead to the precipitation of free alkali, posing a risk of adverse events. Clinical pharmacists' intervention could prevent this interaction. This practice has been shown to be effective, with no subsequent adverse events reported.

Pharmaceutical care of vascular dementia patients with drug-induced liver injury caused by the Compound Congrong Yizhi Capsules: a case report.

BACKGROUND: Drug-induced liver injury (DILI) is a newly discovered adverse drug reaction of Compound Congrong Yizhi Capsules (CCYC) in the treatment of vascular dementia (VD), and targeted pharmaceutical care is urgently needed to be explored. CASE REPORT: DILI was found in a patient who was admitted to the hospital with a diagnosis of VD after treatment with Compound Congrong Yizhi Capsules. According to the guidelines, the patient was initially treated with magnesium isoglycyrrhizinate injection. After 4 days, the clinical pharmacist monitored liver function: alanine aminotransferase (ALT): 153 IU/L, aspartate aminotransferase (AST): 160 IU/L, total bilirubin (TBil): 4.5 µmol/L, and alkaline phosphatase (ALP): 551 IU/L, which indicated that DILI was further aggravated. In addition, the increased blood pressure (156/65 mmHg) indicated the requirement to adjust the medication. Then, the hepatoprotective drugs were adjusted with reduced glutathione combined with ursodeoxycholic acid. After 12 days of treatment, the liver function was significantly improved, the clinical treatment was effective, and the blood pressure was controlled stably with no obvious adverse drug reactions. CONCLUSIONS: With pharmaceutical care guided by clinical pharmacists, the DILI caused by Compound Congrong Yizhi capsules could be reversed to improve the clinical outcome and avoid the occurrence of serious complications.

Effect of pharmaceutical care on the treatment of community-acquired pneumonia in the elderly: a case report.

OBJECTIVE: Elderly patients with community-acquired pneumonia (CAP) have more comorbidities, decreased organ function, and weakened immune function, which can easily lead to various adverse reactionsduring anti-infection treatment. Comprehensive geriatric assessment is a commonly used method to optimize the management of the clinical treatment of the elderly, of which the clinical pharmacists are the core member. However, few studies have focused on the participation of relevant clinical pharmacists of comprehensive geriatric assessment (CGA) of elderly CAP patients. CASE PRESENTATION: A case where the clinical pharmacist participated in the entire process of medical treatment of an elderly patient with CAP. From the first day of admission to the hospital, anti-infective drugs were selected based on the condition combined with the distribution and drug-resistance of common local pathogens, paying attention to the changes of various indicators during treatment, the drug dose was adjusted in time, and targeted anticoagulation, cardiotonic, diuretic, potassium supplementation, intestinal flora regulation and anti-fungal treatment were carried out, as well as the prevention and treatment of antibiotic-related diarrhea. After 24 days of hospitalization, the patient was in a stable condition after treatment and was discharged from the hospital. CONCLUSIONS: The participation of clinical pharmacists in CGA had positive significance for the clinical treatment of elderly CAP, and it was worthy of further improvement and clinical promotion.

Predictors of mechanical ventilation for COVID-19: combined data from three designated hospitals.

OBJECTIVE: Whether patients with COVID-19 require invasive mechanical ventilation (MV) is not yet clear. This article summarizes the clinical treatment process and clinical data of patients with COVID-19 and analyzes the predictive factors for mechanical ventilation for these patients. MATERIALS AND METHODS: A retrospective study was carried out from January 5, 2020, to March 23, 2020, including 98 patients with COVID-19 treated at three designated hospitals in Huangshi City, Hubei Province. Data collection included demographics, previous underlying diseases, clinical manifestations, laboratory examinations, imaging examination results, diagnosis, and prognosis. This study presents a summary of the patients' overall clinical characteristics and clarifies the predictive factors for MV in patients with COVID-19. RESULTS: There were 56 males and 42 females included in this study. The mortality rate was 26.53% (26/98). Fever, cough, and chest tightness were the most common symptoms (64.3%, 37.8%, and 12.2%, respectively). Thirty cases required MV, 30.61% of the total cases, and the mortality rate was 73.33%. The univariate comparison showed that dyspnea, acute physiologic assessment, chronic health evaluation (APACHE II) score, and the ratio between arterial blood oxygen partial pressure (PaO2) and oxygen concentration (FiO2) (P/F) were statistically different between the MV group and the non-MV group (p < 0.05). CONCLUSIONS: Results showed the following: dyspnea; increased white blood cell count; decreased platelets; lowered albumin levels; increased urea nitrogen; increased levels of myocardial enzymes Creatine Kinase (CK), Creatine Kinase, MB Form (CKMB) and lactate dehydrogenase (LDH); increased lactate, and lowered blood calcium tests. These findings may indicate that the patients have an increased probability of needing MV support. A cutoff value for the initial APACHE II score of >11.5 and the initial PaO2/FiO2 ratio of <122.17 mmHg should be considered for MV support for patients with COVID-19.

Genetic selection on abdominal fat content alters the reproductive performance of broilers.

The effects of obesity on reproduction have been widely reported in humans and mice. The present study was designed to compare the reproductive performance of lean and fat chicken lines, divergently selected for abdominal fat content. The following parameters were determined and analyzed in the two lines: (1) reproductive traits, including age at first egg and total egg numbers from generations 14 to 18, absolute and relative testicular weights at 7, 14, 25, 30, 45 and 56 weeks of age, semen quality at 30, 45 and 56 weeks of age in generation 18, and fertility and hatchability from generations 14 to 18; (2) reproductive hormones at 7, 14, 25, 30, 45 and 56 weeks of age in generation 18; (3) and the relative mRNA abundance of genes involved in reproduction at 7, 14, 25, 30, 45 and 56 weeks of age in generation 18. In females, birds in the lean line laid more eggs from the first egg to 40 weeks of age than the birds in the fat line. In male broilers, the birds in the lean line had higher absolute and relative testicular weights at 7, 14 and 25 weeks of age, but lower absolute and relative testicular weights at 56 weeks of age than the birds in the fat line. Male birds in the lean line had greater sperm concentrations and larger numbers of motile and morphologically normal sperms at 30, 45 and 56 weeks of age than the birds in the fat line. Fertility and hatchability were also higher in the lean line than in the fat line. Significant differences in the plasma levels of reproductive hormones and the expression of reproduction-associated genes were also found at different ages in the lean and fat birds, in both males and females. These results suggest that reproductive performance is better in lean birds than in fat birds. In view of the unique divergent lines used in this study, these results imply that selecting for abdominal fat deposition negatively affects the reproductive performance of birds.

Comparative transcriptome analysis reveals three potential antiviral signaling pathways in lymph organ tissue of the red swamp crayfish, Procambarus clarkii.

The red swamp crayfish (Procambarus clarkii) is one of the most economically important farmed aquatic species in China. Compared with its relatively well-known antibacterial and antifungal mechanisms, the antiviral mechanism is still unclear. We used Illumina-based RNA sequencing and bioinformatic technology to obtain high-quality sequence reads from the crayfish lymph organ. A total of 5933 differentially expressed genes (DEGs) were identified between normal and white spot syndrome virus-challenged samples. Of these, 4638 genes were differentially upregulated and 1295 differentially downregulated by more than two-fold. The DEGs were then mapped to different signaling pathways; the Janus kinase/signal transducers and activators of transcription, insulin, and Wnt signaling pathways were predicted to be involved in crayfish antiviral innate immunity. These results provide new insights into crayfish antiviral immunity mechanisms.

A novel lumazine synthase molecule from Brucella significantly promotes the immune-stimulation effects of antigenic protein.

Brucella, an intracellular parasite that infects some livestock and humans, can damage or destroy the reproductive system of livestock. The syndrome is referred to as brucellosis and often occurs in pastoral areas; it is contagious from livestock to humans. In this study, the intact Brucella suis outer membrane protein 31 (omp31) gene was cloned, recombinantly expressed, and examined as a subunit vaccine candidate. The intact Brucella lumazine synthase (bls) gene was cloned and recombinantly expressed to study polymerization function in vitro. Non-reducing gel electrophoresis showed that rBs-BLS existed in different forms in vitro, including as a dimer and a pentamer. An enzyme-linked immunosorbent assay result showed that rOmp31 protein could induce production of an antibody in rabbits. However, the rOmp31-BLS fusion protein could elicit a much higher antibody titer in rabbits; this construct involved fusion of the Omp31 molecule with the BLS molecule. Our results indicate that Omp31 is involved in immune stimulation, while BLS has a polymerizing function based on rOmp31-BLS fusion protein immunogenicity. These data suggest that Omp31 is an ideal subunit vaccine candidate and that the BLS molecule is a favorable transport vector for antigenic proteins.

Comparison of serum biochemical parameters between two broiler chicken lines divergently selected for abdominal fat content.

In humans, obesity is associated with increased or decreased levels of serum biochemical indicators. However, the relationship is not as well understood in chickens. Due to long-term intense selection for fast growth rate, modern broilers have the problem of excessive fat deposition, exhibiting biochemical or metabolic changes. In the current study, the Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF) were used to identify differences in serum biochemical parameters between the 2 lines. A total of 18 serum biochemical indicators were investigated in the 16th, 17th, and 18th generation populations of NEAUHLF, and the genetic parameters of these serum biochemical indicators were estimated. After analyzing the data from these 3 generations together, the results showed that the levels of 16 of the tested serum biochemical parameters were significantly different between the lean and fat birds. In the fat birds, serum concentrations of high-density lipoprotein cholesterol (HDL-C), HDL-C:low-density lipoprotein cholesterol (LDL-C), total bile acid, total protein, albumin, globulin, aspartate transaminase (AST):alanine transaminase (ALT), γ-glutamyl transpeptidase (GGT), uric acid, and creatinine were very significantly higher (P < 0.01), whereas LDL-C, albumin:globulin, glucose, AST, ALT, and free fatty acids concentrations in serum were very significantly lower than those in the lean birds (P < 0.01). Of these 16 serum biochemical parameters, 5 (LDL-C, HDL-C:LDL-C, total bile acid, albumin, and albumin:globulin) had high heritabilities (0.58 ≤ h2 ≤ 0.89), 6 (HDL-C, total protein, globulin, AST:ALT, GGT, and creatinine) had moderate heritabilities (0.29 ≤ h2 ≤ 0.48), and the remaining 5 had low heritabilities (h2 < 0.20). Serum HDL-C, HDL-C:LDL-C, and glucose had higher positive genetic correlation coefficients (rg) with abdominal fat traits (0.30 ≤ rg ≤ 0.80), whereas serum globulin, AST, and uric acid showed higher negative genetic correlations with abdominal fat traits (­0.62 ≤ rg ≤ ­0.30). The remaining 10 serum biochemical parameters had lower genetic correlations with abdominal fat traits (­0.30 < rg < 0.30). In conclusion, we identified serum HDL-C and HDL-C:LDL-C levels as potential biomarkers for selection of lean birds. These findings will also be useful in future studies for investigating obesity and lipid metabolism in humans as well as in other animal species.

Secondary structure estimation and properties analysis of stretched Asian and Caucasian hair.

BACKGROUND: In this previous work, we investigated the secondary structure changes of stretched yak hairs by deconvolution, secondary derivation, and curve fitting and determined the number of bands and their positions in order to resolve the protein spectrum of Raman spectroscopy. OBJECTIVES: The secondary structure estimation and properties analysis of stretched Asian and Caucasian hair were investigated by Fourier transform infrared spectroscopy, tensile curves, and measurement of density. METHODS: The hairs were stretched, dried, and baked at ratios 20%, 40%, 60%, 80% and 100%. RESULTS: The analysis of the amide I band indicated that the transformation from α-helix to ß-pleated structure occurred during the stretching process, which could be verified from the tensile analysis. The cysteine oxide in S-O vibration area exhibited that stretching led to the breakage of the disulfide bonds. When the stretching ratio of Caucasian hair was more than a certain ratio, the fiber macromolecular structure was destroyed because Caucasian hair had finer diameter and less medulla than Asian hair. The ß turn was easier to retract compared with other conformations, resulted in the content increase. The density measurements revealed that the structure of Caucasian hair was indeed more destroyed than that of Asian hair. The cuticles characterization indicated the length of scales was stretched longer and the thickness became thinner. Caucasian hair tended to collapse to form small fragments at the early stage of stretching. With the increase in stretching ratio, the scales of Caucasian hair lifted up, then flaked off and the scale interval increased accordingly. Asian hair was more easily peeled off than Caucasian hair cuticles with the increase in stretching ratio. CONCLUSIONS: The secondary structure of Caucasian hair was destroyed more easily than that of Asian hair.

Effectiveness of olfactory ensheathing cell transplantation for treatment of spinal cord injury.

The aim of this study was to determine the effectiveness and safety of transplantation of olfactory ensheathing cells for functional repair of the spinal cord. An olfactory bulb was obtained from a 4- to 5-month-old aborted fetus, and it was digested into single olfactory ensheathing cells and then cultured and purified for 1 to 2 weeks. Under general anesthesia, these single-cell suspensions of olfactory ensheathing cells were injected into the corresponding spinal injury site with 0.45-mm-diameter injections. The American Spinal Injury Association (ASIA) Impairment Scale was used to evaluate spinal function. A total of 15 patients (12 men, 3 women; age range, 18-56 years; mean age, 40) were admitted for obsolete spinal injuries. Spinal functions of the 15 patients were observed and followed postoperatively for a period ranging from 2 weeks to 1 month. All the 15 patients exhibited improvements in spinal function, and the improvement tendencies continued. Twelve patients had obvious spinal function improvement, and three had slight improvement according to the ASIA scale, with an obvious difference between preoperation and postoperation measures (P < 0.05). No fevers, infections, functional deteriorations, or deaths were seen. Thus, transplantation of olfactory ensheathing cells promoted spinal and neurofunctional recovery in patients with malignant spinal injuries, and this therapeutic method was safe.

Identification of species-specific novel transcripts in pig reproductive tissues using RNA-seq.

Although structural properties of the porcine reproductive system are shared by many placental mammals, some combination of these properties is unique to pigs. To explore whether genomic elements specific to pigs could potentially underlie this uniqueness, we made the first step to identify novel transcripts in two representative pig reproductive tissues by the technique of massively parallel sequencing. To automate the whole process, we built a computational pipeline, which can also be easily extended for similar studies in other species. In total, 5516 and 9061 novel transcripts were found, and 159 and 252 novel transcripts appear to be specific to pigs for the placenta and testis respectively. Furthermore, these novel transcripts were found to be enriched in quantitative trait loci (QTL) regions for reproduction traits in pigs. We validated eight of these novel transcripts by quantitative real-time PCR. With respect to their genomic organization and their functional relationship to reproduction, these transcripts need to be further validated and explored in various pig breeds to better comprehend the relevant aspects of pig physiology that contribute to reproductive performance.

A whole-genome association study for pig reproductive traits.

A whole-genome association study was performed for reproductive traits in commercial sows using the PorcineSNP60 BeadChip and Bayesian statistical methods. The traits included total number born (TNB), number born alive (NBA), number of stillborn (SB), number of mummified foetuses at birth (MUM) and gestation length (GL) in each of the first three parities. We report the associations of informative QTL and the genes within the QTL for each reproductive trait in different parities. These results provide evidence of gene effects having temporal impacts on reproductive traits in different parities. Many QTL identified in this study are new for pig reproductive traits. Around 48% of total genes located in the identified QTL regions were predicted to be involved in placental functions. The genomic regions containing genes important for foetal developmental (e.g. MEF2C) and uterine functions (e.g. PLSCR4) were associated with TNB and NBA in the first two parities. Similarly, QTL in other foetal developmental (e.g. HNRNPD and AHR) and placental (e.g. RELL1 and CD96) genes were associated with SB and MUM in different parities. The QTL with genes related to utero-placental blood flow (e.g. VEGFA) and hematopoiesis (e.g. MAFB) were associated with GL differences among sows in this population. Pathway analyses using genes within QTL identified some modest underlying biological pathways, which are interesting candidates (e.g. the nucleotide metabolism pathway for SB) for pig reproductive traits in different parities. Further validation studies on large populations are warranted to improve our understanding of the complex genetic architecture for pig reproductive traits.

Mapping quantitative trait loci affecting chicken body size traits via genome scanning.

Body size traits reflect the condition of body development, are always mentioned when a breed is described, and are also targets in breeding programmes. In chicken, there are several reports focused on body size traits, such as shank length, tibia length or bone traits. However, no study was carried out on chest width (CW), chest depth (CD), body slope length (BL) and head width (HW) traits. In this study, genome scans were conducted on an F(2) resource population (238 F(2) individuals from 15 full-sib families derived from an intercross of the White Plymouth Rock with the Silkies Fowl) to identify quantitative trait loci (QTL) associated with CW, CD, BL and HW from 7 to 12 weeks of age. In total, 21 significant or suggestive QTL were found that affected four body size traits. Four QTL reached 1% genome-wide significance level: at 297 cM on GGA3 (associated with CW at 9 weeks of age), between 155 and 184 cM on GGA1 (affecting BL traits at 9 and 10 weeks of age), at 22 cM on GGA2 (related with BL traits at 12 weeks of age) and at 36 cM on GGA1 (for HW trait at 8 weeks of age).

An association study of 20 candidate genes with cryptorchidism in Siberian Husky dogs.

Cryptorchidism (CO) as a common developmental defect in purebred dogs causes health concerns of reduced fertility and increases risk of testicular malignancies. A total of 49 single nucleotide polymorphisms (SNPs) discovered from 20 candidate genes was investigated to analyse their associations with CO in Siberian Huskies. The sibling-transmission disequilibrium test on 38 discordant full-sibs revealed seven SNPs in the collagen type II alpha 1 (COL2A1) gene were significantly (p < 0.05) or suggestively (p < 0.10) associated with CO. Further analyses showed that only one SNP (rs23358342) in this gene remained suggestively significant (p < 0.1) on a data set of full-sibs with additional related dogs, but not significant on all 156 Siberian Huskies. Based on the statistical results and the involvement of COL2A1 in the testicle development and descent, we could not exclude COL2A1 as a potential candidate gene for CO in Siberian Huskies. Further studies are necessary to clarify these results from our relatively small sample size.

The Hepatocyte nuclear factor-1 alpha ( HNF1A) gene is associated with fatness and loin muscle area in the pig.

The significance of hepatocyte nuclear factors (HNFs) in ß-cell development and function has been generally recognized in humans, as evidenced by their associations with cases of maturity onset diabetes of the young (MODY). Common Hepatocyte nuclear factor-1 alpha (HNF1A), Hepatocyte nuclear factor-1 beta (HNF1B) and Hepatocyte nuclear factor-4 alpha (HNF4A) mutations could lead to monogenic forms 3, 5 and 1 of diabetes mellitus, respectively, and were characterized by MODY in humans. In this study, multiple variants were discovered in the porcine HNF1A and HNF4A genes, and one single-nucleotide polymorphism (SNP) was detected in the HNF1B gene. Using the Iowa State University Berkshire × Yorkshire pig resource population, the HNF1A, HNF1B and HNF4A genes were mapped on chromosomes 14, 12 and 17, respectively. The linkage disequilibrium (LD) analyses indicated that most of the HNF1A variants were not in strong LD with each other; however, nearly all of them were highly significantly (P < 0.01) associated with loin muscle area (LMA). The SNPs c.327-19G>T and c.1768+40_23del were significantly (P < 0.05) associated with backfat and total lipid percentage, and the latter was also associated with muscle glycogen metabolism measures. Four major haplotypes were observed and the association analyses suggested that haplotype 3 (-CGCGD-, I indicates Insertion and D indicates Deletion) was favorable for reduced backfat, while haplotype 1 (-CACGI-) was unfavorably associated with backfat and LMA. There was no significant interaction effect on backfat among the SNPs c.327-19G>T, c.1768+40_23del of the HNF1A gene and c.646C>T of the transcription factor-7-like 2 (TCF7L2) gene. These findings suggest that the HNF1A gene has significant effects on both fatness- and meat production-related traits. No significant associations with production traits with the SNPs from the HNF1B and HNF4A genes were observed in the study.

A gene-based SNP linkage map for pacific white shrimp, Litopenaeus vannamei.

Pacific white shrimp (Litopenaeus vannamei) are of particular economic importance to the global shrimp aquaculture industry. However, limited genomics information is available for the penaeid species. We utilized the limited public information available, mainly single nucleotide polymorphisms (SNPs) and expressed sequence tags, to discover markers for the construction of the first SNP genetic map for Pacific white shrimp. In total, 1344 putative SNPs were discovered, and out of 825 SNPs genotyped, 418 SNP markers from 347 contigs were mapped onto 45 sex-averaged linkage groups, with approximate coverage of 2071 and 2130 cm for the female and male maps, respectively. The average-squared correlation coefficient (r(2)), a measure of linkage disequilibrium, for markers located more than 50 cm apart on the same linkage group, was 0.15. Levels of r(2) increased with decreasing inter-marker distance from approximately 80 cm, and increased more rapidly from approximately 30 cm. A QTL for shrimp gender was mapped on linkage group 13. Comparative mapping to model organisms, Daphnia pulex and Drosophila melanogaster, revealed extensive rearrangement of genome architecture for L. vannamei, and that L. vannamei was more related to Daphnia pulex. This SNP genetic map lays the foundation for future shrimp genomics studies, especially the identification of genetic markers or regions for economically important traits.

Identification of quantitative trait loci for shank length and growth at different development stages in chicken.

Shank length affects chicken leg health and longer shanks are a source of leg problems in heavy-bodied chickens. Identification of quantitative trait loci (QTL) affecting shank length traits may be of value to genetic improvement of these traits in chickens. A genome scan was conducted on 238 F(2) chickens from a reciprocal cross between the Silky Fowl and the White Plymouth Rock breeds using 125 microsatellite markers to detect static and developmental QTL affecting weekly shank length and growth (from 1 to 12 weeks) in chickens. Static QTL affected shank length from birth to time t, while developmental QTL affected shank growth from time t-1 to time t. Seven static QTL on six chromosomes (GGA2, GGA3, GGA4, GGA7, GGA9 and GGA23) were detected at ages of 2, 3, 4, 5, 6, 7, 9 and 12 weeks, and six developmental QTL on five chromosomes (GGA1, GGA2, GGA4, GGA5 and GGA23) were detected for five shank growth periods, weeks 2-3, 4-5, 5-6, 10-11 and 11-12. A static QTL and a developmental QTL (SQSL1 and DQSL2) were identified at GGA2 (between ADL0190 and ADL0152). SQSL1 explained 2.87-5.30% of the phenotypic variation in shank length from 3 to 7 weeks. DQSL2 explained 2.70% of the phenotypic variance of shank growth between 2 and 3 weeks. Two static and two developmental QTL were involved chromosome 4 and chromosome 23. Two chromosomes (GGA7 and GGA9) had static QTL but no developmental QTL and another two chromosomes (GGA1 and GGA5) had developmental QTL but no static QTL. The results of this study show that shank length and shank growth at different developmental stages involve different QTL.

An evaluation of four candidate genes for use in selection programmes aimed at increased intramuscular fat in Duroc swine.

A sufficient level of intramuscular fat (IMF) is needed to enhance consumer acceptance of pork products, and is currently receiving greater attention within swine genetic improvement programmes. An examination of previously described and novel genetic variants within candidate genes for IMF deposition was performed to evaluate potential use of genetic markers in marker-assisted selection (MAS). Biological candidate genes implicated to play a role in adipogenesis were investigated within two different lines of purebred Duroc pigs. These included MC4R, FABP3, DLK1, and TCF7L2. Significant variation in IMF within the control line was described by the MC4R genotype and a novel BsrfI single nucleotide polymorphism within the FABP3 gene. Genetic markers for DLK1 and TCF7L2 evaluated in this population are not currently recommended for selection in Duroc swine. Existence of MC4R and FABP3 mutations may be useful markers in MAS aimed at IMF improvement, provided that gene effects are segregating and the presence of an association is detected within the population. However, additional work to confirm the use of the investigated genetic markers in selection programmes is needed.

Mapping quantitative trait loci regulating chicken body composition traits.

Genome scans were conducted on an F(2) resource population derived from intercross of the White Plymouth Rock with the Silkies Fowl to detect QTL affecting chicken body composition traits. The population was genotyped with 129 microsatellite markers and phenotyped for 12 body composition traits on 238 F(2) individuals from 15 full-sib families. In total, 21 genome-wide QTL were found to be responsible for 11 traits, including two newly studied traits of proventriculus weight and shank girth. Three QTL were genome-wide significant: at 499 cm on GGA1 (explained 3.6% of phenotypic variance, P < 0.01) and 51 cm on GGA5 (explained 3.3% of phenotypic variance, P < 0.05) for the shank & claw weight and 502 cm on GGA1 (explained 1.4% of phenotypic variance, P < 0.05) for wing weight. The QTL on GGA1 seemed to have pleiotropic effects, also affecting gizzard weight at 490 cm, shank girth at 489 cm and intestine length at 481 cm. It is suggested that further efforts be made to understand the possible pleiotropic effects of the QTL on GGA1 and that on GGA5 for two shank-related traits.

SNP discovery in Litopenaeus vannamei with a new computational pipeline.

Litopenaeus vannamei (Pacific white shrimp) have been farmed in the Americas for many years and are growing in popularity in Asia with the development of specific pathogen-free stocks. The full genomic sequence of this species might not be available in the near future, so other tools are needed to discover the location of polymorphic sites for quantitative trait loci mapping, association studies and subsequent marker-assisted selection. Currently, 25 937 L. vannamei expressed sequence tags (ESTs) are publicly available. These sequences were manually screened, masked for tandem repeats and inputted into CAP3 for clustering. The resulting 3532 contigs were analysed for possible single nucleotide polymorphisms (SNPs) with SNPIDENTIFIER, a newly developed computer program for predicting SNPs. SNPIDENTIFIER is designed for ESTs without accompanying chromatogram sequence quality information, and therefore it performs quality control checks on all data. SNPIDENTIFIER sets a threshold such that the sequences used have a poor quality nucleotide (N) frequency <0.1, and it trims off the first 10 bases of every sequence to ensure higher sequence quality. For a base to be predicted as an SNP, the minor nucleotide (allele) frequency must be >0.1, it must be observed at least four times and the 15 bases on either side must exactly match the consensus sequence. Using these conservative parameters, 504 SNPs were predicted from 141 contigs for L. vannamei. A small sample of 18 individuals from three lines have been sequenced to verify prediction results and 17 of 39 (44%) of the tested SNPs have been confirmed.