1
|
Park J, Wickramasinghe S, Mills DA, Lönnerdal BL, Ji P. Iron Fortification and Inulin Supplementation in Early Infancy: Evaluating the Impact on Iron Metabolism and Trace Mineral Status in a Piglet Model. Curr Dev Nutr 2024; 8:102147. [PMID: 38645881 PMCID: PMC11026733 DOI: 10.1016/j.cdnut.2024.102147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/18/2024] [Accepted: 03/22/2024] [Indexed: 04/23/2024] Open
Abstract
Background Infant formula in the United States contains abundant iron, raising health concerns about excess iron intake in early infancy. Objectives Using a piglet model, we explored the impact of high iron fortification and prebiotic or synbiotic supplementation on iron homeostasis and trace mineral bioavailability. Methods Twenty-four piglets were stratified and randomly assigned to treatments on postnatal day 2. Piglets were individually housed and received an iron-adequate milk diet (AI), a high-iron milk diet (HI), HI supplemented with 5% inulin (HI with a prebiotic [HIP]), or HIP with an oral gavage of Ligilactobacillus agilis YZ050, an inulin-fermenting strain, every third day (HI with synbiotic [HIS]). Milk was provided in 14 meals daily, mimicking formula feeding in infants. Fecal consistency score and body weight were recorded daily or every other day. Blood and feces were sampled weekly, and tissues collected on postnatal day 29. Data were analyzed using mixed model analysis of variance with repeated measures whenever necessary. Results Diet did not affect growth. HI increased hemoglobin, hematocrit, and serum iron compared to AI. Despite marginal adequacy, AI upregulated iron transporter genes and maintained satisfactory iron status in most pigs. HI upregulated hepcidin gene expression in liver, caused pronounced tissue iron deposition, and markedly increased colonic and fecal iron. Inulin supplementation, regardless of L. agilis YZ050, not only attenuated hepatic iron overload but also decreased colonic and fecal iron without altering pH or the expression of iron regulatory genes. HI lowered zinc (Zn) and copper (Cu) in the duodenum and liver compared to AI, whereas HIP and HIS further decreased Zn and Cu in the liver and diminished colonic and fecal trace minerals. Conclusions Early-infancy excessive iron fortification causes iron overload and compromises Zn and Cu absorption. Inulin decreases trace mineral absorption likely by enhancing gut peristalsis and stool frequency.
Collapse
Affiliation(s)
- Jungjae Park
- Department of Nutrition, University of California Davis, CA, United States
| | - Saumya Wickramasinghe
- Department of Food Science and Technology, University of California Davis, CA, United States
| | - David A. Mills
- Department of Food Science and Technology, University of California Davis, CA, United States
| | - Bo L. Lönnerdal
- Department of Nutrition, University of California Davis, CA, United States
| | - Peng Ji
- Department of Nutrition, University of California Davis, CA, United States
| |
Collapse
|
2
|
L. G. S. L, Wickramasinghe S, P. A. B. D. A, Abbas K, Hussain T, Ramasamy S, Manomohan V, Tapsoba ASR, Pichler R, Babar ME, Periasamy K. Indigenous cattle of Sri Lanka: Genetic and phylogeographic relationship with Zebu of Indus Valley and South Indian origin. PLoS One 2023; 18:e0282761. [PMID: 37585485 PMCID: PMC10431622 DOI: 10.1371/journal.pone.0282761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 07/30/2023] [Indexed: 08/18/2023] Open
Abstract
The present study reports the population structure, genetic admixture and phylogeography of cattle breeds of Sri Lanka viz. Batu Harak, Thawalam and White cattle. Moderately high level of genetic diversity was observed in all the three Sri Lankan zebu cattle breeds. Estimates of inbreeding for Thawalam and White cattle breeds were relatively high with 6.1% and 7.2% respectively. Genetic differentiation of Sri Lankan Zebu (Batu Harak and White cattle) was lowest with Red Sindhi among Indus Valley Zebu while it was lowest with Hallikar among the South Indian cattle. Global F statistics showed 6.5% differences among all the investigated Zebu cattle breeds and 1.9% differences among Sri Lankan Zebu breeds. The Sri Lankan Zebu cattle breeds showed strong genetic relationships with Hallikar cattle, an ancient breed considered to be ancestor for most of the Mysore type draught cattle breeds of South India. Genetic admixture analysis revealed high levels of breed purity in Lanka White cattle with >97% Zebu ancestry. However, significant taurine admixture was observed in Batu Harak and Thawalam cattle. Two major Zebu haplogroups, I1 and I2 were observed in Sri Lankan Zebu with the former predominating the later in all the three breeds. A total of 112 haplotypes were observed in the studied breeds, of which 50 haplotypes were found in Sri Lankan Zebu cattle. Mismatch analysis revealed unimodal distribution in all the three breeds indicating population expansion. The sum of squared deviations (SSD) and raggedness index were non-significant in both the lineages of all the three breeds except for I1 lineage of Thawalam cattle (P<0.01) and I2 lineage of Batu Harak cattle (P<0.05). The results of neutrality tests revealed negative Tajima's D values for both the lineages of Batu Harak (P>0.05) and White cattle (P>0.05) indicating an excess of low frequency polymorphisms and demographic expansion. Genetic dilution of native Zebu cattle germplasm observed in the study is a cause for concern. Hence, it is imperative that national breeding organizations consider establishing conservation units for the three native cattle breeds to maintain breed purity and initiate genetic improvement programs.
Collapse
Affiliation(s)
- Lokugalappatti L. G. S.
- Animal Production and Health Section, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria
- Faculty of Veterinary Medicine and Animal Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - Saumya Wickramasinghe
- Faculty of Veterinary Medicine and Animal Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - Alexander P. A. B. D.
- Faculty of Veterinary Medicine and Animal Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - Kamran Abbas
- Animal Production and Health Section, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria
- Department of Molecular Biology, Virtual University of Pakistan, Lahore, Pakistan
| | - Tanveer Hussain
- Department of Molecular Biology, Virtual University of Pakistan, Lahore, Pakistan
| | - Saravanan Ramasamy
- Department of Animal Genetics and Breeding, Veterinary College and Research Institute, Namakkal, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Vandana Manomohan
- Animal Production and Health Section, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria
- Department of Animal Genetics and Breeding, Veterinary College and Research Institute, Namakkal, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Arnaud Stephane R. Tapsoba
- Animal Production and Health Section, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria
- Laboratoire de Biologie et de Santé Animale (LaBioSA), Institut de l’Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
| | - Rudolf Pichler
- Animal Production and Health Section, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria
| | - Masroor E. Babar
- Department of Animal Sciences, The University of Agriculture, Dera Ismail Khan, Khyber Pakhtunkhwa, Pakistan
| | - Kathiravan Periasamy
- Animal Production and Health Section, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria
| |
Collapse
|
3
|
Edirithilake T, Nanayakkara N, Lin XX, Biggs PJ, Chandrajith R, Lokugalappatti S, Wickramasinghe S. Urinary MicroRNA Analysis Indicates an Epigenetic Regulation of Chronic Kidney Disease of Unknown Etiology in Sri Lanka. Microrna 2023; 12:156-163. [PMID: 36733246 DOI: 10.2174/2211536612666230202152932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 11/02/2022] [Accepted: 11/29/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND Chronic kidney disease of unknown etiology (CKDu) is reported among male paddy farmers in the dry zone of Sri Lanka. The exact cause of this disease remains undetermined. Genetic susceptibility is identified as a major risk factor for CKDu Objectives: In this study, small urinary RNAs were characterized in CKDu patients, healthy endemic and non-endemic controls. Differently expressed urinary miRNAs and their associated pathways were identified in the study population. METHODS Healthy and diseased male volunteers (n = 9) were recruited from Girandurukotte (endemic) and Mawanella (non-endemic) districts. Urinary small RNAs were purified and sequenced using Illumina MiSeqTM. The sequence trace files were assembled and analyzed. Differentially ex-pressed miRNAs among these three groups were identified and pathway analysis was conducted. RESULTS The urine samples contained 130,623 sequence reads identified as non-coding RNAs, PIWI-interacting RNAs (piRNA), and miRNAs. Approximately four percent of the total small RNA reads represented miRNA, and 29% represented piRNA. A total of 409 miRNA species were ex-pressed in urine. Interestingly, both diseased and endemic controls population showed significantly low expression of miRNA and piRNA. Regardless of the health status, the endemic population ex-pressed significantly low levels of miR-10a, miR-21, miR-148a, and miR-30a which have been linked with several environmental toxins Conclusion: Significant downregulation of miRNA and piRNA expression in both diseased and healthy endemic samples indicates an epigenetic regulation of CKDu involving genetic and environmental interaction. Further studies of specific miRNA species are required to develop a miRNA panel to identify individuals susceptible to CKDu.
Collapse
Affiliation(s)
- Thanuri Edirithilake
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine and Animal Science, University of Peradeniya, Peradeniya 20400, Sri Lanka
| | | | - Xiao Xiao Lin
- Massey Genome Service, School of Natural Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Patrick J Biggs
- Molecular Epidemiology & Public Health Laboratory (mEpiLab), Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North, 4442, New Zealand
- School of Natural Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Rohana Chandrajith
- Department of Geology, Faculty of Science, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - Sampath Lokugalappatti
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine and Animal Science, University of Peradeniya, Peradeniya 20400, Sri Lanka
| | - Saumya Wickramasinghe
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine and Animal Science, University of Peradeniya, Peradeniya 20400, Sri Lanka
- Department of Food Science and Technology, University of California, Davis, 95616, USA
| |
Collapse
|
4
|
Wickramaratne S, de Silva N, Wickramasinghe S, Wanigasekara A, Adhikari R, Rajapakasha E. Olfactory Behaviour Reactions to Acalypha indica Preparations in Domestic Cats. Appl Anim Behav Sci 2022. [DOI: 10.1016/j.applanim.2022.105776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
5
|
Rupasinghe R, Smith WA, Harvey DJ, Wickramasinghe S, Rajapaksha E. Response of adult domestic cats in Sri Lanka to Acalypha indica root embedded toys and the influence of single nucleotide polymorphisms in olfactory receptor genes on the elicited behavior. Appl Anim Behav Sci 2022. [DOI: 10.1016/j.applanim.2022.105677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
6
|
Rajawardana DU, Fernando PC, Biggs PJ, Namali Hewajulige IG, Nanayakkara CM, Wickramasinghe S, Lin XX, Berry L. An insight into tropical milk microbiome: Bacterial community composition of cattle milk produced in Sri Lanka. Int Dairy J 2022. [DOI: 10.1016/j.idairyj.2021.105266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
7
|
Wang H, Simpson JH, Kotra ME, Zhu Y, Wickramasinghe S, Mills DA, Chiu NHL. Epitranscriptomic profile of Lactobacillus agilis and its adaptation to growth on inulin. BMC Res Notes 2021; 14:154. [PMID: 33883017 PMCID: PMC8058956 DOI: 10.1186/s13104-021-05563-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 04/09/2021] [Indexed: 12/17/2022] Open
Abstract
Objective Ribonucleic acids (RNA) are involved in many cellular functions. In general, RNA is made up by only four different ribonucleotides. The modifications of RNA (epitranscriptome) can greatly enhance the structural diversity of RNA, which in turn support some of the RNA functions. To determine whether the epitranscriptome of a specific probiotic is associated with its adaptation to the source of energy, Lactobacillus agilis (YZ050) was selected as a model and its epitranscriptome was profiled and compared by using mass spectrometry. Results The L. agilis epitranscriptome (minus rRNA modifications) consists of 17 different RNA modifications. By capturing the L. agilis cells during exponential growth, reproducible profiling was achieved. In a comparative study, the standard source of energy (glucose) in the medium was substituted by a prebiotic inulin, and a downward trend in the L. agilis epitranscriptome was detected. This marks the first report on a system-wide variation of a bacterial epitranscriptome that resulted from adapting to an alternative energy source. No correlation was found between the down-regulated RNA modifications and the expression level of corresponding writer genes. Whereas, the expression level of a specific exonuclease gene, RNase J1, was detected to be higher in cells grown on inulin.
Collapse
Affiliation(s)
- Hongzhou Wang
- Department of Chemistry and Biochemistry, University of North Carolina Greensboro, Greensboro, NC, USA
| | - Jennifer H Simpson
- Department of Chemistry and Biochemistry, University of North Carolina Greensboro, Greensboro, NC, USA
| | - Madison E Kotra
- Department of Chemistry and Biochemistry, University of North Carolina Greensboro, Greensboro, NC, USA
| | - Yuanting Zhu
- Department of Food Science and Technology, University of California, Davis, CA, USA
| | | | - David A Mills
- Department of Food Science and Technology, University of California, Davis, CA, USA
| | - Norman H L Chiu
- Department of Chemistry and Biochemistry, University of North Carolina Greensboro, Greensboro, NC, USA. .,Joint School of Nanoscience and Nanoengineering, University of North Carolina Greensboro, Greensboro, NC, USA.
| |
Collapse
|
8
|
M Pry J, Jackson W, Rupasinghe R, Lishanthe G, Badurdeen Z, Abeysekara T, Chandrajith R, Smith W, Wickramasinghe S. A pilot case-control study using a one health approach to evaluate behavioral, environmental, and occupational risk factors for chronic kidney disease of unknown etiology in Sri Lanka. One Health Outlook 2021; 3:4. [PMID: 33829142 PMCID: PMC8011406 DOI: 10.1186/s42522-020-00034-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 12/29/2020] [Indexed: 05/17/2023]
Abstract
BACKGROUND Chronic kidney disease of unknown etiology (CKDu) was first recognized in Sri Lanka in the early 1990s, and since then it has reached epidemic levels in the North Central Province of the country. The prevalence of CKDu is reportedly highest among communities that engage in chena and paddy farming, which is most often practiced in the dry zone including the North Central and East Central Provinces of Sri Lanka. Previous studies have suggested varied hypotheses for the etiology of CKDu; however, there is not yet a consensus on the primary risk factors, possibly due to disparate study designs, sample populations, and methodologies. METHODS The goal of this pilot case-control study was to evaluate the relationships between key demographic, cultural, and occupational variables as risk factors for CKDu, with a primary interest in pesticide exposure both occupationally and through its potential use as an ingredient in brewed kasippu alcohol. An extensive one health focused survey was developed with in cooperation with the Centre for Research, Education, and Training on Kidney Diseases of Sri Lanka. RESULTS A total of 56 CKDu cases and 54 control individuals were surveyed using a proctored, self-reported questionnaire. Occupational pesticide exposure and alcohol consumption were not found to be significant risk factors for CKDu. However, a statistically significant association with CKDu was observed with chewing betel (adjusted odds ratio [aOR]: 6.11, 95% confidence interval [CI]: 1.93, 19.35), age (aOR: 1.07, 95% CI: 1.02, 1.13), owning a pet dog (aOR: 3.74, 95% CI: 1.38, 10.11), water treatment (aOR: 3.68, 95% CI: 1.09, 12.43) and pests in the house (aOR: 5.81, 95% CI: 1.56, 21.60). CONCLUSIONS The findings of this study suggest future research should focus on practices associated with chewing betel, potential animal interactions including pests in the home and pets, and risk factors associated with water. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1186/s42522-020-00034-3.
Collapse
Affiliation(s)
- Jake M Pry
- Implementation Science Unit, Centre for Infectious Disease Research Zambia (CIDRZ), 10101 Lusaka, Zambia
- School of Medicine, Washington University, St. Louis, MO USA
| | - Wendi Jackson
- School of Veterinary Medicine, University of California, Davis, USA
| | | | | | - Zied Badurdeen
- Center for Research and Training on Kidney Diseases (CERTKiD), Faculty of Medicine, University of Peradeniya, Kandy, Sri Lanka
| | - Tilak Abeysekara
- Center for Research and Training on Kidney Diseases (CERTKiD), Faculty of Medicine, University of Peradeniya, Kandy, Sri Lanka
| | | | - Woutrina Smith
- School of Veterinary Medicine, University of California, Davis, USA
| | - Saumya Wickramasinghe
- School of Veterinary Medicine, University of California, Davis, USA
- Faculty of Veterinary Medicine and Animal Science, University of Peradeniya, Kandy, Sri Lanka
| |
Collapse
|
9
|
Rajapaksha C, Amarasinghe AP, Fernando S, Rajapakse RPVJ, Tappe D, Wickramasinghe S. Morphological and molecular description of Armillifer moniliformis larvae isolated from Sri Lankan brown palm civet (Paradoxurus montanus). Parasitol Res 2020; 119:773-781. [PMID: 31897786 DOI: 10.1007/s00436-019-06581-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 12/18/2019] [Indexed: 11/24/2022]
Abstract
We report Armillifer moniliformis species infecting the endemic Sri Lankan brown palm civet (Paradoxurus montanus) from the Knuckles Range Forest Conservation Area, Sri Lanka. Larval stages of A. moniliformis were found during the postmortem of three civet cats found dead. Morphological studies were done by a light microscope and a scanning electron microscope (SEM). Histopathological examination was conducted using tissue samples obtained from the liver. For the molecular analysis, DNA was extracted from the isolated third-stage larvae. The NADH dehydrogenase subunit 5 (ND5) and the second internal transcribed spacer region (ITS-2), a portion of the large subunit nuclear ribosomal DNA (28S), a portion of 18S ribosomal rRNA gene (18S), and cytochrome c oxidase subunit 1 gene (COX1) were amplified using polymerase chain reaction (PCR). Excysted third-stage larvae were observed in the lungs, omentum, the pleural cavity, the abdominal cavity, and the surface of the spleen and the pericardium. Around 88 third-stage larvae were isolated from three civet cats. First-stage larvae in the liver were surrounded by outer fibrous layer over the inner germinal layer and filled with clear fluid. Slight hemorrhage, leukocyte infiltration, and mild hepatocellular degeneration in the liver were observed. The SEM examination indicated the unique oral apparatus comprises the oval-shaped mouth opening in between two pairs of curved, retractile hamuli. The sequences obtained for ND5, ITS-2, 28S, 18S, and COX1 were 301, 382, 325, 414, and 644 bp in length respectively. Morphology, sequence similarity search, sequence alignment, and phylogenetic analysis identified this parasite as A. moniliformis.
Collapse
Affiliation(s)
- C Rajapaksha
- Department of Parasitology, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka.,Digital Banking Unit, Commercial Bank of Ceylon PLC, Colombo, 06, Sri Lanka
| | - A P Amarasinghe
- Department of Parasitology, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka
| | - S Fernando
- Department of Zoology, Faculty of Natural Sciences, The Open University of Sri Lanka, Nawala, Nugegoda, Sri Lanka
| | - R P V J Rajapakse
- Department of Veterinary Pathobiology, Faculty of Veterinary Medicine and Animal Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - D Tappe
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - S Wickramasinghe
- Department of Parasitology, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka.
| |
Collapse
|
10
|
Boudry G, Hamilton MK, Chichlowski M, Wickramasinghe S, Barile D, Kalanetra KM, Mills DA, Raybould HE. Bovine milk oligosaccharides decrease gut permeability and improve inflammation and microbial dysbiosis in diet-induced obese mice. J Dairy Sci 2017; 100:2471-2481. [PMID: 28131576 DOI: 10.3168/jds.2016-11890] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 11/28/2016] [Indexed: 12/20/2022]
Abstract
Obesity is characterized by altered gut homeostasis, including dysbiosis and increased gut permeability closely linked to the development of metabolic disorders. Milk oligosaccharides are complex sugars that selectively enhance the growth of specific beneficial bacteria in the gastrointestinal tract and could be used as prebiotics. The aim of the study was to demonstrate the effects of bovine milk oligosaccharides (BMO) and Bifidobacterium longum ssp. infantis (B. infantis) on restoring diet-induced obesity intestinal microbiota and barrier function defects in mice. Male C57/BL6 mice were fed a Western diet (WD, 40% fat/kcal) or normal chow (C, 14% fat/kcal) for 7 wk. During the final 2 wk of the study, the diet of a subgroup of WD-fed mice was supplemented with BMO (7% wt/wt). Weekly gavage of B. infantis was performed in all mice starting at wk 3, yet B. infantis could not be detected in any luminal contents when mice were killed. Supplementation of the WD with BMO normalized the cecal and colonic microbiota with increased abundance of Lactobacillus compared with both WD and C mice and restoration of Allobaculum and Ruminococcus levels to that of C mice. The BMO supplementation reduced WD-induced increase in paracellular and transcellular flux in the large intestine as well as mRNA levels of the inflammatory marker tumor necrosis factor α. In conclusion, BMO are promising prebiotics to modulate gut microbiota and intestinal barrier function for enhanced health.
Collapse
Affiliation(s)
- Gaëlle Boudry
- INRA UR1341 Alimentation, Adaptations Digestives, Nerveuses et Comportementales, Saint-Gilles, France F-35590.
| | - M Kristina Hamilton
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis 95616
| | - Maciej Chichlowski
- Department of Food Science and Technology, University of California, Davis 95616
| | | | - Daniela Barile
- Department of Food Science and Technology, University of California, Davis 95616; Foods for Health Institute, University of California, Davis 95616
| | - Karen M Kalanetra
- Department of Food Science and Technology, University of California, Davis 95616; Foods for Health Institute, University of California, Davis 95616
| | - David A Mills
- Department of Food Science and Technology, University of California, Davis 95616; Foods for Health Institute, University of California, Davis 95616
| | - Helen E Raybould
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis 95616; Foods for Health Institute, University of California, Davis 95616
| |
Collapse
|
11
|
Jackson W, Pry J, Wickramasinghe S, Rupasinghe R, Jayawickrama S, Badurdeen Z, Chadrajith R, Smith W. Utilizing a One Health approach for identifying risk factors associated
with an epidemic of chronic kidney disease of unknown etiology (CKDu) in the
North Central region of Sri Lanka. Ann Glob Health 2016. [DOI: 10.1016/j.aogh.2016.04.651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
|
12
|
Luke N, Wickramasinghe S, Sebastiampillai B, Gunathilake M, Miththinda N, Fernando S, Silva S, Premaratna R. Antibiotic sensitivity patterns among ESBL UTIs in Sri Lanka. Int J Infect Dis 2016. [DOI: 10.1016/j.ijid.2016.02.283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
13
|
Abstract
This review lists the currently known species of millepedes in Sri Lanka and discusses their current taxonomic status and distribution based on previous studies from 1865 to date. A total of 104 millipede species belonging to 44 genera, 18 families and nine orders have been recorded in Sri Lanka. Of these, 82 are known only from Sri Lanka; additionally, nine genera and one family are known only from Sri Lanka. Most of the millipede species have been recorded from two localities, namely Pundaluoya and Kandy in the central highlands of Sri Lanka. Current knowledge on the taxonomy, evolutionary relationships, distribution and conservation of the millipedes of Sri Lanka is still limited and scattered. Thus we suggest more intensive surveys to acquire comprehensive data on the millipedes of Sri Lanka.
Collapse
Affiliation(s)
- H K S De Zoysa
- Department of Biological Sciences, Faculty of Applied Sciences, Rajarata University of Sri Lanka.;
| | - Anh D Nguyen
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, No.18, Hoangquocviet Rd., Hanoi, Vietnam.;
| | - S Wickramasinghe
- Department of Biological Sciences, Faculty of Applied Sciences, Rajarata University of Sri Lanka.;
| |
Collapse
|
14
|
Wickramasinghe S, Pacheco AR, Lemay DG, Mills DA. Bifidobacteria grown on human milk oligosaccharides downregulate the expression of inflammation-related genes in Caco-2 cells. BMC Microbiol 2015; 15:172. [PMID: 26303932 PMCID: PMC4548914 DOI: 10.1186/s12866-015-0508-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 08/13/2015] [Indexed: 12/15/2022] Open
Abstract
Background Breastfed human infants are predominantly colonized by bifidobacteria that thrive on human milk oligosaccharides (HMO). Two predominant species of bifidobacteria in infant feces are Bifidobacterium breve (B. breve) and Bifidobacterium longum subsp. infantis (B. infantis), both of which include avid HMO-consumer strains. Our laboratory has previously shown that B. infantis, when grown on HMO, increases adhesion to intestinal cells and increases the expression of the anti-inflammatory cytokine interleukin-10. The purpose of the current study was to investigate the effects of carbon source—glucose, lactose, or HMO—on the ability of B. breve and B. infantis to adhere to and affect the transcription of intestinal epithelial cells on a genome-wide basis. Results HMO-grown B. infantis had higher percent binding to Caco-2 cell monolayers compared to B. infantis grown on glucose or lactose. B. breve had low adhesive ability regardless of carbon source. Despite differential binding ability, both HMO-grown strains significantly differentially affected the Caco-2 transcriptome compared to their glucose or lactose grown controls. HMO-grown B. breve and B. infantis both downregulated genes in Caco-2 cells associated with chemokine activity. Conclusion The choice of carbon source affects the interaction of bifidobacteria with intestinal epithelial cells. HMO-grown bifidobacteria reduce markers of inflammation, compared to glucose or lactose-grown bifidobacteria. In the future, the design of preventative or therapeutic probiotic supplements may need to include appropriately chosen prebiotics. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0508-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Saumya Wickramasinghe
- Department of Basic Veterinary Sciences, University of Peradeniya, Peradeniya, 20400, Sri Lanka. .,Foods for Health Institute University of California, Davis, Davis, CA, 95616, USA. .,Department of Viticulture and Enology, University of California, Davis, Davis, CA, 95616, USA.
| | - Alline R Pacheco
- Foods for Health Institute University of California, Davis, Davis, CA, 95616, USA. .,Department of Food Science and Technology, University of California, Davis, Davis, CA, 95616, USA. .,Department of Viticulture and Enology, University of California, Davis, Davis, CA, 95616, USA.
| | - Danielle G Lemay
- Foods for Health Institute University of California, Davis, Davis, CA, 95616, USA. .,Genome Center, University of California, Davis, Davis, CA, 95616, USA.
| | - David A Mills
- Foods for Health Institute University of California, Davis, Davis, CA, 95616, USA. .,Department of Food Science and Technology, University of California, Davis, Davis, CA, 95616, USA. .,Department of Viticulture and Enology, University of California, Davis, Davis, CA, 95616, USA.
| |
Collapse
|
15
|
|
16
|
Khaldi N, Vijayakumar V, Dallas D, Guerrero A, Wickramasinghe S, Smilowitz JT, Medrano JF, Lebrilla C, Shields DC, German JB. Predicting the important enzymes in human breast milk digestion. J Agric Food Chem 2014; 62:7225-7232. [PMID: 24620897 PMCID: PMC4264622 DOI: 10.1021/jf405601e] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 03/12/2014] [Accepted: 03/12/2014] [Indexed: 05/31/2023]
Abstract
Human milk is known to contain several proteases, but little is known about whether these enzymes are active, which proteins they cleave, and their relative contribution to milk protein digestion in vivo. This study analyzed the mass spectrometry-identified protein fragments found in pooled human milk by comparing their cleavage sites with the enzyme specificity patterns of an array of enzymes. The results indicate that several enzymes are actively taking part in the digestion of human milk proteins within the mammary gland, including plasmin and/or trypsin, elastase, cathepsin D, pepsin, chymotrypsin, a glutamyl endopeptidase-like enzyme, and proline endopeptidase. Two proteins were most affected by enzyme hydrolysis: β-casein and polymeric immunoglobulin receptor. In contrast, other highly abundant milk proteins such as α-lactalbumin and lactoferrin appear to have undergone no proteolytic cleavage. A peptide sequence containing a known antimicrobial peptide is released in breast milk by elastase and cathepsin D.
Collapse
Affiliation(s)
- Nora Khaldi
- Conway Institute of Biomolecular
and Biomedical Research, School
of Medicine and Medical Sciences and Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Republic of Ireland
- Department of Food Science and Technology, Foods for Health Institute, Department of Chemistry, and Department of
Animal Science, University of California, Davis, California 95616, United States
| | - Vaishnavi Vijayakumar
- Conway Institute of Biomolecular
and Biomedical Research, School
of Medicine and Medical Sciences and Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Republic of Ireland
| | - David
C. Dallas
- Department of Food Science and Technology, Foods for Health Institute, Department of Chemistry, and Department of
Animal Science, University of California, Davis, California 95616, United States
| | - Andrés Guerrero
- Department of Food Science and Technology, Foods for Health Institute, Department of Chemistry, and Department of
Animal Science, University of California, Davis, California 95616, United States
| | - Saumya Wickramasinghe
- Department of Food Science and Technology, Foods for Health Institute, Department of Chemistry, and Department of
Animal Science, University of California, Davis, California 95616, United States
- Department
of Basic Veterinary Sciences, University
of Peradeniya, Peradeniya 20400, Sri Lanka
| | - Jennifer T. Smilowitz
- Department of Food Science and Technology, Foods for Health Institute, Department of Chemistry, and Department of
Animal Science, University of California, Davis, California 95616, United States
| | - Juan F. Medrano
- Department of Food Science and Technology, Foods for Health Institute, Department of Chemistry, and Department of
Animal Science, University of California, Davis, California 95616, United States
| | - Carlito
B. Lebrilla
- Department of Food Science and Technology, Foods for Health Institute, Department of Chemistry, and Department of
Animal Science, University of California, Davis, California 95616, United States
| | - Denis C. Shields
- Conway Institute of Biomolecular
and Biomedical Research, School
of Medicine and Medical Sciences and Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Republic of Ireland
| | - J. Bruce German
- Department of Food Science and Technology, Foods for Health Institute, Department of Chemistry, and Department of
Animal Science, University of California, Davis, California 95616, United States
| |
Collapse
|
17
|
Corrigan A, Walker JL, Wickramasinghe S, Hernandez MA, Newhouse SJ, Folarin AA, Lewis CM, Sanderson JD, Spicer J, Marinaki AM. Pharmacogenetics of pemetrexed combination therapy in lung cancer: pathway analysis reveals novel toxicity associations. Pharmacogenomics J 2014; 14:411-7. [DOI: 10.1038/tpj.2014.13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 01/17/2014] [Accepted: 02/19/2014] [Indexed: 02/01/2023]
|
18
|
|
19
|
Corrigan A, Lal R, Wickramasinghe S, Whelan S, Sanderson J, Marinaki A, Spicer J. 31 Testing for association between TPMT, COMT and NOX3 variants and the onset of ototoxicity in lung cancer patients treated with platinum chemotherapy. Lung Cancer 2013. [DOI: 10.1016/s0169-5002(13)70031-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
20
|
Wickramasinghe S, Rincon G, Islas-Trejo A, Medrano JF. Transcriptional profiling of bovine milk using RNA sequencing. BMC Genomics 2012; 13:45. [PMID: 22276848 PMCID: PMC3285075 DOI: 10.1186/1471-2164-13-45] [Citation(s) in RCA: 180] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 01/25/2012] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Cow milk is a complex bioactive fluid consumed by humans beyond infancy. Even though the chemical and physical properties of cow milk are well characterized, very limited research has been done on characterizing the milk transcriptome. This study performs a comprehensive expression profiling of genes expressed in milk somatic cells of transition (day 15), peak (day 90) and late (day 250) lactation Holstein cows by RNA sequencing. Milk samples were collected from Holstein cows at 15, 90 and 250 days of lactation, and RNA was extracted from the pelleted milk cells. Gene expression analysis was conducted by Illumina RNA sequencing. Sequence reads were assembled and analyzed in CLC Genomics Workbench. Gene Ontology (GO) and pathway analysis were performed using the Blast2GO program and GeneGo application of MetaCore program. RESULTS A total of 16,892 genes were expressed in transition lactation, 19,094 genes were expressed in peak lactation and 18,070 genes were expressed in late lactation. Regardless of the lactation stage approximately 9,000 genes showed ubiquitous expression. Genes encoding caseins, whey proteins and enzymes in lactose synthesis pathway showed higher expression in early lactation. The majority of genes in the fat metabolism pathway had high expression in transition and peak lactation milk. Most of the genes encoding for endogenous proteases and enzymes in ubiquitin-proteasome pathway showed higher expression along the course of lactation. CONCLUSIONS This is the first study to describe the comprehensive bovine milk transcriptome in Holstein cows. The results revealed that 69% of NCBI Btau 4.0 annotated genes are expressed in bovine milk somatic cells. Most of the genes were ubiquitously expressed in all three stages of lactation. However, a fraction of the milk transcriptome has genes devoted to specific functions unique to the lactation stage. This indicates the ability of milk somatic cells to adapt to different molecular functions according to the biological need of the animal. This study provides a valuable insight into the biology of lactation in the cow, as well as many avenues for future research on the bovine lactome.
Collapse
|
21
|
Barboza M, Pinzon J, Wickramasinghe S, Froehlich JW, Moeller I, Smilowitz JT, Ruhaak LR, Huang J, Lönnerdal B, German JB, Medrano JF, Weimer BC, Lebrilla CB. Glycosylation of human milk lactoferrin exhibits dynamic changes during early lactation enhancing its role in pathogenic bacteria-host interactions. Mol Cell Proteomics 2012; 11:M111.015248. [PMID: 22261723 DOI: 10.1074/mcp.m111.015248] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Human milk lactoferrin (hmLF) is the most abundant glycoprotein present in human milk and displays a broad range of protective functions in the gut of newborn infants. hmLF is N-glycosylated, but little is known about the lactation stage-related development of the glycosylation phenotype. hmLF glycosylation from milk samples from five donors during the first 10 weeks of lactation was assessed and observed to be more diverse than previously reported. During this period dynamic changes in glycosylation were observed corresponding to a decrease in glycosylation in the second week followed by an increase in total glycosylation as well as higher order fucosylation thereafter. Gene expression analysis was performed in milk somatic cells from a sixth subject. It was found that fucosyltransferase expression increased during entire period, whereas expression of genes for the oligosaccharyl transferase complex decreased in the second week. The effect of hmLF glycosylation was examined for the protein's ability to affect bacterial binding to epithelial cells. hmLF significantly inhibited pathogen adhesion and purified hmLF glycans significantly reduced Salmonella invasion of colonic epithelial cells to levels associated with non-invasive deletion mutants. This study indicates that hmLF glycosylation is tightly regulated by gene expression and that glyco-variation is involved in modulating pathogen association.
Collapse
Affiliation(s)
- Mariana Barboza
- Department of Chemistry, Functional Glycobiology Program, University of California Davis. One Shields Ave, Davis, California 95616, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Abstract
Sialic acid, a nine-carbon sugar acid usually is present in the non-reducing terminal position of free oligosaccharides and glycoconjugates. Sialylated conjugates in mammals perform important roles in cellular recognition, signaling, host-pathogen interaction and neuronal development. Metabolism of sialylated conjugates involves a complex pathway consisting of enzymes distributed among the different compartments in the cell. These enzymes are encoded by 32 genes diversely distributed throughout the mammalian genome. Genetic variants in some of these genes are associated with embryonic lethality and abnormal phenotypes in mice and neuromuscular diseases, carcinomas and immune-mediated diseases in humans. In humans, the CMP-NeuAc-hydroxylase (CMAH) enzyme is inactivated due to a deletion mutation in the encoded enzyme. This lack of Neu5Gc phenotype makes humans unique among mammals. This review focuses on genes encoding enzymes in sialic acid metabolism pathways in mammalian cells with special emphasis on the human, mouse and cow.
Collapse
Affiliation(s)
- Saumya Wickramasinghe
- Department of Animal Science, University of California-Davis, One Shields Ave., Davis, CA 95616-8521, USA
| | | |
Collapse
|
23
|
Wickramasinghe S, Rincon G, Medrano JF. Variants in the pregnancy-associated plasma protein-A2 gene on Bos taurus autosome 16 are associated with daughter calving ease and productive life in Holstein cattle. J Dairy Sci 2011; 94:1552-8. [PMID: 21338820 DOI: 10.3168/jds.2010-3237] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Accepted: 11/15/2010] [Indexed: 01/29/2023]
Abstract
Reproductive disorders in dairy herds have a negative effect on farm profitability and sustainability of milk production. Given the substantial evidence of the role of the pregnancy-associated plasma protein (PAPP) gene family in the regulation of reproduction in humans and mice, its role in insulin-like growth factor metabolism, quantitative trait loci effects in the mouse, and location of a calving ease QTL on bovine chromosome 16, the PAPP-A2 gene was chosen as a candidate gene to perform an association study for reproductive health in cattle. Single nucleotide polymorphisms (SNP) were identified in coding and conserved noncoding regions of the PAPP-A2 gene in 3 dairy breeds. A total of 7 tag SNP were genotyped in 662 Holstein bulls (UCD-bulls) to perform marker trait association analysis. Three SNP (SNP 13, 15, and 16) were in strong linkage disequilibrium in Holsteins, showing significant positive associations with daughter calving ease, productive life, milk yield, and protein yield. These results were validated by genotyping SNP15 in a larger population of 992 bulls from the cooperative dairy DNA repository (CDDR-bulls). Our results demonstrate that the PAPP-A2 gene is associated with reproductive health in Holstein cattle and that the identified SNP can be used as genetic markers in dairy breeding due to their positive association with reproductive and productive traits. Functional studies need to be conducted to identify the mechanisms for the association of SNP with these traits.
Collapse
Affiliation(s)
- S Wickramasinghe
- Department of Animal Science, University of California, Davis, California 95616-8521, USA
| | | | | |
Collapse
|
24
|
Wickramasinghe S, Hua S, Rincon G, Islas-Trejo A, German JB, Lebrilla CB, Medrano JF. Transcriptome profiling of bovine milk oligosaccharide metabolism genes using RNA-sequencing. PLoS One 2011; 6:e18895. [PMID: 21541029 PMCID: PMC3081824 DOI: 10.1371/journal.pone.0018895] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 03/24/2011] [Indexed: 12/21/2022] Open
Abstract
This study examines the genes coding for enzymes involved in bovine milk oligosaccharide metabolism by comparing the oligosaccharide profiles with the expressions of glycosylation-related genes. Fresh milk samples (n = 32) were collected from four Holstein and Jersey cows at days 1, 15, 90 and 250 of lactation and free milk oligosaccharide profiles were analyzed. RNA was extracted from milk somatic cells at days 15 and 250 of lactation (n = 12) and gene expression analysis was conducted by RNA-Sequencing. A list was created of 121 glycosylation-related genes involved in oligosaccharide metabolism pathways in bovine by analyzing the oligosaccharide profiles and performing an extensive literature search. No significant differences were observed in either oligosaccharide profiles or expressions of glycosylation-related genes between Holstein and Jersey cows. The highest concentrations of free oligosaccharides were observed in the colostrum samples and a sharp decrease was observed in the concentration of free oligosaccharides on day 15, followed by progressive decrease on days 90 and 250. Ninety-two glycosylation-related genes were expressed in milk somatic cells. Most of these genes exhibited higher expression in day 250 samples indicating increases in net glycosylation-related metabolism in spite of decreases in free milk oligosaccharides in late lactation milk. Even though fucosylated free oligosaccharides were not identified, gene expression indicated the likely presence of fucosylated oligosaccharides in bovine milk. Fucosidase genes were expressed in milk and a possible explanation for not detecting fucosylated free oligosaccharides is the degradation of large fucosylated free oligosaccharides by the fucosidases. Detailed characterization of enzymes encoded by the 92 glycosylation-related genes identified in this study will provide the basic knowledge for metabolic network analysis of oligosaccharides in mammalian milk. These candidate genes will guide the design of a targeted breeding strategy to optimize the content of beneficial oligosaccharides in bovine milk.
Collapse
Affiliation(s)
- Saumya Wickramasinghe
- Department of Animal Science, University of California Davis, Davis, California, United States of America
| | - Serenus Hua
- Department of Chemistry, University of California Davis, Davis, California, United States of America
| | - Gonzalo Rincon
- Department of Animal Science, University of California Davis, Davis, California, United States of America
| | - Alma Islas-Trejo
- Department of Animal Science, University of California Davis, Davis, California, United States of America
| | - J. Bruce German
- Department of Food Science and Technology, University of California Davis, Davis, California, United States of America
| | - Carlito B. Lebrilla
- Department of Chemistry, University of California Davis, Davis, California, United States of America
| | - Juan F. Medrano
- Department of Animal Science, University of California Davis, Davis, California, United States of America
- * E-mail:
| |
Collapse
|
25
|
Cánovas A, Rincon G, Islas-Trejo A, Wickramasinghe S, Medrano JF. SNP discovery in the bovine milk transcriptome using RNA-Seq technology. Mamm Genome 2010; 21:592-8. [PMID: 21057797 PMCID: PMC3002166 DOI: 10.1007/s00335-010-9297-z] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Accepted: 10/14/2010] [Indexed: 11/28/2022]
Abstract
High-throughput sequencing of RNA (RNA-Seq) was developed primarily to analyze global gene expression in different tissues. However, it also is an efficient way to discover coding SNPs. The objective of this study was to perform a SNP discovery analysis in the milk transcriptome using RNA-Seq. Seven milk samples from Holstein cows were analyzed by sequencing cDNAs using the Illumina Genome Analyzer system. We detected 19,175 genes expressed in milk samples corresponding to approximately 70% of the total number of genes analyzed. The SNP detection analysis revealed 100,734 SNPs in Holstein samples, and a large number of those corresponded to differences between the Holstein breed and the Hereford bovine genome assembly Btau4.0. The number of polymorphic SNPs within Holstein cows was 33,045. The accuracy of RNA-Seq SNP discovery was tested by comparing SNPs detected in a set of 42 candidate genes expressed in milk that had been resequenced earlier using Sanger sequencing technology. Seventy of 86 SNPs were detected using both RNA-Seq and Sanger sequencing technologies. The KASPar Genotyping System was used to validate unique SNPs found by RNA-Seq but not observed by Sanger technology. Our results confirm that analyzing the transcriptome using RNA-Seq technology is an efficient and cost-effective method to identify SNPs in transcribed regions. This study creates guidelines to maximize the accuracy of SNP discovery and prevention of false-positive SNP detection, and provides more than 33,000 SNPs located in coding regions of genes expressed during lactation that can be used to develop genotyping platforms to perform marker-trait association studies in Holstein cattle.
Collapse
Affiliation(s)
- Angela Cánovas
- IRTA, Genètica i Millora Animal, 191 Alcalde Rovira Roure Av, 25198, Lleida, Spain
| | | | | | | | | |
Collapse
|
26
|
Devi KR, Narain K, Agatsuma T, Blair D, Nagataki M, Wickramasinghe S, Yatawara L, Mahanta J. Morphological and molecular characterization of Paragonimus westermani in northeastern India. Acta Trop 2010; 116:31-8. [PMID: 20493821 DOI: 10.1016/j.actatropica.2010.05.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2009] [Revised: 05/04/2010] [Accepted: 05/09/2010] [Indexed: 11/26/2022]
Abstract
Evidence for the presence of lung flukes of the Paragonimus westermani in India remains scant. In particular, evidence based on morphology of adult worms is lacking. Metacercariae of the genus Paragonimus, recovered from crabs in two regions of northeastern India, were raised to adulthood in laboratory rats. Morphologically, these worms appear to be P. westermani. DNA sequences from the second internal transcribed spacer (ITS2) and a portion of the ribosomal large subunit gene (28S) of the nuclear ribosomal RNA gene repeat, as well as fragments of the mitochondrial cytochrome c oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 1 (nad1) genes, all supported this identification. Molecular phylogenetic methods were used for studying the relatedness of these Indian flukes with counterparts from southeast and far-east Asia. Molecular data showed that Indian representatives of the P. westermani complex represent a distinct lineage. It is unclear whether the Indian form can cause disease in humans as some members of the complex do elsewhere.
Collapse
|
27
|
Perera A, Wickramasinghe S, Perera BJ, Somaratne P. Reliable and easy identification of bacterial acute respiratory infections of childhood. Ceylon Med J 1998; 43:200-5. [PMID: 10355173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
OBJECTIVES To identify the causative bacteria in childhood acute respiratory infections (ARI) and to determine the usefulness of pus cell counts in differentiating between pathogenic and commensal bacteria, cultured from nasopharyngeal aspirates. DESIGN Case control prospective study. SETTING Outpatients' department and the paediatric unit at General Hospital, Colombo South. SUBJECTS 200 children under 5 years with cough and difficulty in breathing for less than one week who had no history of antibiotic therapy for the current illness, and 50 healthy controls matched for age and sex. RESULTS 56.5% of cases had bacterial infections. Branhamella catarrhalis (25%), Haemophilus influenzae (12.5%) and Streptococcus pneumoniae (10.5%) were the major pathogens identified. Pus cell counts were found to be significantly higher in cases than in controls (X2 58.28 df = 1 p < 0.001), and the pathogens were more often associated with pus cell counts of more than 10/field. CONCLUSIONS 56.5% of children with ARI had bacterial infections. B catarrhalis seems to play a major role in childhood ARI. Examination of nasopharyngeal aspirates is a useful way to identify pathogens, provided microscopic examination for pus cells is performed together with culture.
Collapse
Affiliation(s)
- A Perera
- Department of Community Medicine and Family Medicine, Faculty of Medical Sciences, University of Sri Jayawardenepura
| | | | | | | |
Collapse
|
28
|
Affiliation(s)
- D C Rees
- MRC Molecular Haematology Unit, Institute of Molecular Medicine, Oxford, United Kingdom
| | | | | | | | | |
Collapse
|
29
|
Rees DC, Luo LY, Thein SL, Singh BM, Wickramasinghe S. Nontransfusional iron overload in thalassemia: association with hereditary hemochromatosis. Blood 1997; 90:3234-6. [PMID: 9376610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
|
30
|
Vafiadis P, Bennett ST, Todd JA, Nadeau J, Grabs R, Goodyer CG, Wickramasinghe S, Colle E, Polychronakos C. Insulin expression in human thymus is modulated by INS VNTR alleles at the IDDM2 locus. Nat Genet 1997; 15:289-92. [PMID: 9054944 DOI: 10.1038/ng0397-289] [Citation(s) in RCA: 552] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Type 1 diabetes or insulin-dependent diabetes mellitus (IDDM) is due to autoimmune destruction of pancreatic beta-cells. Genetic susceptibility to IDDM is encoded by several loci, one of which (IDDM2) maps to a variable number of tandem repeats (VNTR) minisatellite, upstream of the insulin gene (INS). The short class I VNTR alleles (26-63 repeats) predispose to IDDM, while class III alleles (140-210 repeats) have a dominant protective effect. We have reported that, in human adult and fetal pancreas in vivo, class III alleles are associated with marginally lower INS mRNA levels than class I, suggesting transcriptional effects of the VNTR. These may be related to type 1 diabetes pathogenesis, as insulin is the only known beta-cell specific IDDM autoantigen. In search of a more plausible mechanism for the dominant effect of class III alleles, we analysed expression of insulin in human fetal thymus, a critical site for tolerance induction to self proteins. Insulin was detected in all thymus tissues examined and class III VNTR alleles were associated with 2- to 3-fold higher INS mRNA levels than class I. We therefore propose higher levels of thymic INS expression, facilitating immune tolerance induction, as a mechanism for the dominant protective effect of class III alleles.
Collapse
Affiliation(s)
- P Vafiadis
- McGill University-Montreal Children's Hospital Research Institute, Montréal, Québec, Canada
| | | | | | | | | | | | | | | | | |
Collapse
|