Haplotype-based breeding: A new insight in crop improvement

Haplotype-based breeding (HBB) is one of the cutting-edge technologies in the realm of crop improvement due to the increasing availability of Single Nucleotide Polymorphisms identified by Next Generation Sequencing technologies. The complexity of the data can be decreased with fewer statistical tests and a lower probability of spurious associations by combining thousands of SNPs into a few hundred haplotype blocks. The presence of strong genomic regions in breeding lines of most crop species facilitates the use of haplotypes to improve the efficiency of genomic and marker-assisted selection. Haplotype-based breeding as a Genomic Assisted Breeding (GAB) approach harnesses the genome sequence data to pinpoint the allelic variation used to hasten the breeding cycle and circumvent the challenges associated with linkage drag. This review article demonstrates ways to identify candidate genes, superior haplotype identification, haplo-pheno analysis, and haplotype-based marker-assisted selection. The crop improvement strategies that utilize superior haplotypes will hasten the breeding progress to safeguard global food security.

Exogenous delivery of dsRNA for management of mungbean yellow mosaic virus on blackgram

MAIN CONCLUSION

Exogenous application of dsRNA molecules targeting MYMV genes offers a promising approach to effectively mitigate yellow mosaic disease in blackgram, demonstrating potential for sustainable plant viral disease management. The exogenous application of double-stranded RNA (dsRNA) molecules to control plant viral diseases is gaining traction due to its advantages over conventional methods, such as target specificity, non-polluting nature, and absence of residue formation. Furthermore, this approach does not involve genome modification. In this study, dsRNA molecules targeting the coat protein gene (dsCP) and replication initiator protein gene (dsRep) of mungbean yellow mosaic virus (MYMV) were synthesised using an in vitro transcription method. To evaluate the effectiveness of dsRNA treatment, blackgram plants exhibiting MYMV symptoms at the first trifoliate stage were subjected to exogenous application of dsRNA. Second, third, and fourth trifoliate leaves, which emerged at 7, 15, and 21 days after dsRNA application, respectively, were monitored for MYMV symptoms. Remarkably, a significant reduction in yellow mosaic disease (YMD) symptoms was observed in the newly emerged trifoliate leaves of MYMV-infected blackgram plants after treatment with dsRNA targeting both gene regions. This reduction was evident as a decrease in the intensity of yellow mosaic coverage on the leaf lamina compared to control. dsCP effectively reduced the MYMV titre in the treated plants for up to 15 days. However, dsRep demonstrated greater efficiency in conferring resistance to MYMV at 15 days post-application. These findings were supported by quantitative real-time PCR analysis, where the observed Ct values for DNA extracted from dsRep-treated plants were significantly higher compared to the Ct values of DNA from dsCP-treated plants at 15 days post-application. Similarly, higher viral copy numbers were observed in dsCP-treated plants 15 days after dsRNA treatment, in contrast to plants treated with dsRep.

Guesstimate of thymoquinone diversity in Nigella sativa L. genotypes and elite varieties collected from Indian states using HPTLC technique

Thymoquinone is a valuable metabolite derived from the Nigella sativa L. seeds and has a variety of therapeutic properties. Thymoquinone was estimated using n-hexane:ethyl acetate (8:2, v/v) green solvent system and computed at a wavelength of 254 nm using the high-performance thin-layer chromatography densitometry method in distinct varieties and genotypes congregated from different geographical regions. Genotype Ajmer Nigella-13 has the paramount thymoquinone content (247.60 µg/100 mg seed) followed by Ajmer Nigella 19 (244.5 µg/100 mg seed), while the lowest amount of thymoquinone was recorded in the genotype Ajmer Nigella-6 (42.88 µg/100 mg seed). The hierarchical cluster analysis found that the collected genotypes and elite varieties were classified into four broad clusters, and the identified chemotypes with elevated thymoquinone proportion were positioned in cluster D. Significant genotypic variation in thymoquinone content is available, that can be used in exploiting pharmaceutical applications of N. sativa L. as well as a breeding programme for specific metabolite improvement perspective.

Variation in biochemical, physiological and ecophysiological traits among the teak (Tectona grandis Linn. f) seed sources of India

Teak being an iconic timber species the studies on its physiological and biochemical traits are very limited in India and worldwide. As a result, the current study aimed to assess biochemical parameters such as chlorophyll a, chlorophyll b, total chlorophyll, carotenoids, chlorophyll ab ratio, proline content, and peroxidase activity, along with physiological parameters such as Chlorophyll stability index, relative water content, and leaf area, as well as ecophysiological traits such as net photosynthetic rate (Pn), stomatal conductance (Gs), intercellular CO₂ concentration (Ci), transpiration rate (Tr), Leaf temperature, intrinsic water-use efficiency (iWUE), instantaneous water use efficiency and intrinsic carboxylation efficiency of thirty teak seed sources collected from different states of India. FCRITK 19, FCRITK 21, FCRITK 25, FCRITK 29, and FCRITK 05 were reported to have a greater photosynthetic rate (> 17 µmol m⁻² s⁻¹) coupled with a relative water content of more than 50% and a chlorophyll stability index of more than 60%, which could be used in a future genetic improvement programme. Correlation analysis indicated that water use efficiency was found to be strongly but negatively correlated with transpiration rate (−0.601) and stomatal conductance (−0.910). The proline content had a substantial positive correlation with the chlorophyll stability index (0.890), signifying that they are associated with abiotic stress conditions. Cluster analysis was attempted to discriminate the sources based on biochemical, physiological and ecophysiological traits. Eleven sources (FCRITK 25, FCRITK 27, FCRITK 29, FCRITK 14, FCRITK 30, FCRITK 16, FCRITK 05, FCRITK 13, FCRITK 02, FCRITK 17 and FCRITK 15) exhibited superior performance compared to rest of the sources.

Identification of major candidate genes for multiple abiotic stress tolerance at seedling stage by network analysis and their validation by expression profiling in rice (Oryza sativa L.)

A wealth of microarray and RNA-seq data for studying abiotic stress tolerance in rice exists but only limited studies have been carried out on multiple stress-tolerance responses and mechanisms. In this study, we identified 6657 abiotic stress-responsive genes pertaining to drought, salinity and heat stresses from the seedling stage microarray data of 83 samples and used them to perform unweighted network analysis and to identify key hub genes or master regulators for multiple abiotic stress tolerance. Of the total 55 modules identified from the analysis, the top 10 modules with 8-61 nodes comprised 239 genes. From these 10 modules, 10 genes common to all the three stresses were selected. Further, based on the centrality properties and highly dense interactions, we identified 7 intra-modular hub genes leading to a total of 17 potential candidate genes. Out of these 17 genes, 15 were validated by expression analysis using a panel of 4 test genotypes and a pair of standard check genotypes for each abiotic stress response. Interestingly, all the 15 genes showed upregulation under all stresses and in all the genotypes, suggesting that they could be representing some of the core abiotic stress-responsive genes. More pertinently, eight of the genes were found to be co-localized with the stress-tolerance QTL regions. Thus, in conclusion, our study not only provided an effective approach for studying abiotic stress tolerance in rice, but also identified major candidate genes which could be further validated by functional genomics for abiotic stress tolerance.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03182-7.

Can Scoliotic Discs Be Controls for Molecular Studies in Intervertebral Disc Research? Insights From Proteomics

STUDY DESIGN

Proteomic analysis of human intervertebral discs.

OBJECTIVES

To compare the characters of scoliotic discs and discs from magnetic resonance imaging (MRI)-normal voluntary organ donors controls used in disc research employing proteomics and establish "true controls" that can be utilized for future intervertebral disc (IVD) research.

METHODS

Eight MRI-normal discs from 8 brain-dead voluntary organ donors (ND) and 8 scoliotic discs (SD) from 3 patients who underwent anterior surgery for adolescent idiopathic scoliosis were subjected to tandem mass spectrometry, and further analysis was performed.

RESULTS

Mass spectrometry identified a total of 235 proteins in ND and 438 proteins in the SD group. Proteins involved in extracellular matrix integrity (Versican, keratins KRT6A, KRT14, KRT5, and KRT 13A1, A-kinase anchor protein 13, coagulation factor XIII A chain, proteoglycan 4) and proteins involved in transcription and DNA repair (Von Willebrand factor A domain-containing 3B, eukaryotic initiation factor 2B, histone H4, leukocyte cell-derived chemotaxin 2) were found to be downregulated in SD. Inflammatory proteins (C3, C1S), and oxidative stress response proteins (peroxiredoxin-2,6, catalase, myeloperoxidase, apolipoprotein E) were found to be upregulated in SD. These changes were reflected at the pathway level also.

CONCLUSION

Findings of our study confirm that scoliotic discs have an abundance of inflammatory, oxidative stress response proteins, which are either absent or downregulated in the ND group indicating that scoliotic discs are not pathologically inert. Furthermore, this study has established MRI-normal discs from voluntary organ donors as the "true" control for molecular studies in IVD research.

Biohardening of Banana cv. Karpooravalli (ABB; Pisang Awak) With Bacillus velezensis YEBBR6 Promotes Plant Growth and Reprograms the Innate Immune Response Against Fusarium oxysporum f.sp. cubense

Induction of innate immune response and growth promotion in banana by B. velezensis against Foc.

Modic changes are associated with activation of intense inflammatory and host defense response pathways - molecular insights from proteomic analysis of human intervertebral discs

BACKGROUND CONTEXT

Patients with modic changes (MC) form a distinct clinical subset with reports of higher intensity of pain, poor clinical and surgical outcomes and higher incidence of recurrence. MC also is an independent risk factor for increased post-operative surgical site infection.

PURPOSE

This study aimed to investigate the biological changes at molecular level, in discs with MCs. We also aim to identify biological biomarkers and potential targets for molecular therapy.

STUDY DESIGN

Experimental analysis MATERIALS AND METHODS: Nucleus pulposus (NP) from 24 patients undergoing microdiscectomy for disc herniation [14 discs with MC and 10 without modic changes (NMC)] were procured. The overall expression of proteins, biological processes, protein-protein and metabolite interactions were analysed and compared. Host defense response proteins (HDRPs) and immunological pathways activated in patients with MC were documented and analysed.

RESULTS

Label-free proteomic approach with stringent filters revealed a total of 208 proteins in MC and 193 in NMC groups. 45 proteins were specific to MC; 30 to NMC and 163 common to both. Downregulated proteins in MC belonged to components of extracellular matrix such as collagens (COL- 6A1, 6A2, 6A3, 11A1, 12A1, and 20A1), and proteoglycans (versican (VCAN), and biglycan (BGN)). Inflammatory molecules [plasminogen (PLG), angiogenin (ANG), fibroblast growth factor-binding protein 2 (FGFBP2), tetranectin (CLEC3B), cartilage acidic protein 1(CRTAC1), kininogen (KNG-1), chitinase-3-like protein 2 (CHI3L2), and ferritin (FTL) were expressed only in the MC group. The significantly altered pathways in MC included Fc Fragment of IgG Receptor IIIa (FCGR3A)-mediated phagocytosis, regulation of Toll-like receptors (TLR) by endogenous ligand, neutrophil and platelet degranulation. 50 HDRPs were identified in the study, 14 of which were specific to MC and included acute phase reactants, antimicrobial peptides, complement cascade proteins, inflammatory molecule and stress response proteins. Metabolite-protein interaction analysis revealed a significant interaction between 19 proteins, specifically involving ubiquitin mediating proteasome degradative pathway and an association with the metabolite-glutamic acid in the MC group. Accumulation of glutamic acid in MC discs was confirmed by quantitative amino acid analysis using High-performance liquid chromatography.

CONCLUSION

Our study confirms that MC represents an intense inflammatory status and activation of host defense response and immunological pathways. Downstream effects leading to ubiquitin mediated proteasomal degradation of ECM proteins and the resulting metabolites such as glutamic acid could cause excessive pain and needs further investigation.

CLINICAL SIGNIFICANCE

We have documented the expression of inflammatory molecules, immune mechanisms and host defense response proteins which throw molecular insights into the pathological mechanisms of MC. Further, ubiquitin mediated proteasomal degradation and accumulation of glutamate in discs with MC might serve as targets for molecular therapy.

Subclinical infection can be an initiator of inflammaging leading to degenerative disk disease: evidence from host-defense response mechanisms

PURPOSE

There is considerable controversy on the role of genetics, mechanical and environmental factors, and, recently, on subclinical infection in triggering inflammaging leading to disk degeneration. The present study investigated sequential molecular events in the host, analyzing proteome level changes that will reveal triggering factors of inflammaging and degeneration.

METHODS

Ten MRI normal disks (ND) from braindead organ donors and 17 degenerated disks (DD) from surgery were subjected to in-gel-based label-free ESI-LC-MS/MS analysis. Bacterial-responsive host-defense response proteins/pathways leading to Inflammaging were identified and compared between ND and DD.

RESULTS

Out of the 263 well-established host-defense response proteins (HDRPs), 243 proteins were identified, and 64 abundantly expressed HDRPs were analyzed further. Among the 21 HDRPs common to both ND and DD, complement factor 3 (C3) and heparan sulfate proteoglycan 2 (HSPG2) were significantly upregulated, and lysozyme (LYZ), superoxide dismutase 3 (SOD3), phospholipase-A2 (PLA2G2A), and tissue inhibitor of metalloproteinases 3 (TIMP-3) were downregulated in DD. Forty-two specific HDRPs mainly, complement proteins, apolipoproteins, and antimicrobial proteins involved in the complement cascade, neutrophil degranulation, and oxidative-stress regulation pathways representing an ongoing host response to subclinical infection and uncontrolled inflammation were identified in DD. Protein-Protein interaction analysis revealed cross talk between most of the expressed HDRPs, adding evidence to bacterial presence and stimulation of these defense pathways.

CONCLUSIONS

The predominance of HDRPs involved in complement cascades, neutrophil degranulation, and oxidative-stress regulation indicated an ongoing infection mediated inflammatory process in DD. Our study has documented increasing evidence for bacteria's role in triggering the innate immune system leading to chronic inflammation and degenerative disk disease.

Assessment of Antioxidant Potential of Lutein, a Retinol Equivalent Carotenoid in Medicinal Landrace of Rice ‘Kavuni’

Background: Indigenous traditional coloured rices are rich in dietary fibre, resistant starch, minerals, bioactive compounds and antioxidants like anthocyanins, luteins and phenols. Kavuni is one such brownish black medical landrace of rice considered as nutrition supplement since 400BC as it cures gastritis, peptic ulcer and also enhances blood circulation and known for its anti diabetic and anti-inflammatory properties. Lutein is the only dietary oxycarotenoid found in both the macula and lens of the human eye, and acts as blocker of blue light damage, quench reactive oxygen species, prevent age related macular degeneration, cataracts, cardiovascular disease and lung cancer. Aim: The objective of the present investigation was to characterize the lutein content and antioxidant potential of Kavuni and released mega varieties of rice (ASD 16, Swarna Sub1) and its derivatives obtained from crosses ASD 16 and Kavuni; Swarna Sub1 and Kavuni. Methodology & Results: It was found that lutein (quantified by HPLC) was much higher in Kavuni (225 µg/100 g) compared with white rice varieties (ASD 16-15 µg/100g and Swarna Sub1-21 µg/100 g) and the DPPH (2, 2-diphenyl-1-picrylhydrazyl) scavenging ability (for quantification of antioxidant potential) were in the order (Kavuni >>ASD16, Swarna Sub1. Pigmented grain genotypes having higher lutein content had higher percentage of free radical scavenging activity of DPPH and lower IC50 values compared to non pigmented genotypes. Conclusion: It is conceivable that the medicinal landraces of rice could be exploited as one of the potential sources for plant - based pharmaceutical products.

Environmental impact of phytic acid in Maize (Zea mays. L) genotypes for the identification of stable inbreds for low phytic acid

Phytic acid is a ubiquitous compound that chelates the micronutrients in food and hinder their absorption. Hence, breeding for low phytate content for producing stable low phytic acid (lpa) hybrids is essential. Phytic acid content in maize grains has been found to vary across environments and its stable expression has yet to be explored. In a view of this, forty inbreds were screened with two checks viz., CO-6 and CO-H(M)-8 across three locations. Twenty morphological and three quality traits were observed to identify the stable lines for low phytic acid with higher free inorganic phosphorous and starch. Among all the lines, UMI-467, LPA-2-285, LPA-2-395 and UMI-447 recorded a stable performance in both AMMI and GGE biplot analysis for low phytic acid (2.52-3.32 mg/g). These lines also had a higher free inorganic phosphorous, ensuring its bioavailability (1.78-1.88 mg/g). There were perturbations in yield, starch and seed characteristics of the stable low phytic acid lines due to their lower phytic acid concentrations. This stated the role of phytic acid in plant physiology and established the constraints to be faced in breeding for low phytic acid in maize. Among the lpa lines, LPA-2-285 (57.83%) and UMI-447 (55.78%) had the highest average starch content. The lowest stable phytic acid content was observed in UMI-467 (2.52 mg/g) and this line had severe reductions in yield parameters. Considering the seed and yield characteristics, LPA-2-285, LPA-2-395 and UMI-447 performed better than UMI-467. Although these four stable lines were poor in their adaptability among all the genotypes, they could be utilised as promising stable donors to facilitate the development of stable lpa hybrids.

Inflammaging determines health and disease in lumbar discs-evidence from differing proteomic signatures of healthy, aging, and degenerating discs

BACKGROUND CONTEXT

The true understanding of aging and disc degeneration (DD) is still elusive. MRI has not helped our attempts to understand the health and disease status of the discs as it reflects mainly the end morphologic changes and not the changes at a molecular level. Understanding degeneration at a molecular level through proteomics might allow differentiation from normal aging and also aid in the development of biomarkers for early diagnosis and preventive therapies.

PURPOSE

To utilize proteomics to understand the molecular basis of healthy, aging, and degenerating discs and conclusively differentiate normal aging and degeneration.

STUDY DESIGN

Proteomic analysis of human intervertebral disc samples.

METHODS

L4-L5 disc samples from three groups were acquired and subjected to proteomic analysis. Samples from individuals aged in the second, third, and fourth decades were used to represent young healthy discs (Group A). Those from MRI normal donors aged in the fifth, sixth, and seventh decades represented normal aging (Group B). Five degenerated discs obtained from patients at surgery represented degeneration (Group C). The entire proteome map and alteration in protein expressions were further analyzed using bioinformatics analysis. This was a self-funded project.

RESULTS

There were 84 common proteins. Specific proteins numbered 225 in A, 315 in B, and 283 in C. By gene ontology biological process identification, Group A predominated with extracellular matrix organization, cytoskeletal structural and normal metabolic proteins. Group B differed in having additional basal expression of immune response, complement inhibitors, and senescence proteins. Group C was different, with upregulation of proteins associated with oxidative stress response, positive regulators of apoptosis, innate immune response, complement activation and defense response to gram positive bacteria indicating ongoing inflammaging.

CONCLUSIONS

Our study documented diverse proteome signatures between the young, aging and degenerating discs. Inflammaging was the main differentiator between normal biological aging and DD.

CLINICAL SIGNIFICANCE

Multiple inflammatory molecules unique to DD were identified, allowing the possibility of developing specific biomarkers for early diagnosis and thereby provide evidence-based metrics for preventive measures rather than surgical intervention and also to monitor progress of the disease.

A Rare Survival in Celphos Poisoning

Aluminium phosphide poisoning releases phosphine gas which causes inhibition of cytochrome oxidase, inhibition of electron transport chain and thereby myocardial suppression. It is known to cause various electric abnormalities in the heart from ST-T depression to fatal tachyarrhythmias. Here we present a case of celphos poisoning presenting with both supraventricular tachycardia and ventricular tachycardia.

Development and Genetic Characterization of A Novel Herbicide (Imazethapyr) Tolerant Mutant in Rice (Oryza sativa L.)

BACKGROUND

Increased water and labour scarcity in major rice growing areas warrants a shift towards direct seeded rice cultivation under which management of weeds is a major issue. Use of broad spectrum non-selective herbicides is an efficient means to manage weeds. Availability of rice genotypes with complete tolerance against broad-spectrum non-selective herbicides is a pre-requisite for advocating use of such herbicides. In the present study, we developed an EMS induced rice mutant, 'HTM-N22', exhibiting tolerance to a broad spectrum herbicide, 'Imazethapyr', and identified the mutations imparting tolerance to the herbicide.

RESULTS

We identified a stable and true breeding rice mutant, HTM-N22 (HTM), tolerant to herbicide, Imazethapyr, from an EMS-mutagenized population of approximately 100,000 M2 plants of an upland rice variety, Nagina 22 (N22). Analysis of inheritance of herbicide tolerance in a cross between Pusa 1656-10-61/HTM showed that this trait is governed by a single dominant gene. To identify the causal gene for Imazethapyr tolerance, bulked segregant analysis (BSA) was followed using microsatellite markers flanking the three putative candidate genes viz., an Acetolactate Synthase (ALS) on chromosome 6 and two Acetohydroxy Acid Synthase (AHAS) genes, one on chromosomes 2 and another on chromosome 4. RM 6844 on chromosome 2 located 0.16 Mbp upstream of AHAS (LOC_Os02g30630) was found to co-segregate with herbicide tolerance. Cloning and sequencing of AHAS (LOC_Os02g30630) from the wild type, N22 and the mutant HTM and their comparison with reference Nipponbare sequence revealed several Single Nucleotide Polymorphisms (SNPs) in the mutant, of which eight resulted in non-synonymous mutations. Three of the eight amino acid substitutions were identical to Nipponbare and hence were not considered as causal changes. Of the five putative candidate SNPs, four were novel (at positions 30, 50, 81 and 152) while the remaining one, S627D was a previously reported mutant, known to result in Imidazolinone tolerance in rice. Of the novel ones, G152E was found to alter the hydrophobicty and abolish an N myristoylation site in the HTM compared to the WT, from reference based modeling and motif prediction studies.

CONCLUSIONS

A novel mutant tolerant to the herbicide "Imazethapyr" was developed and characterized for genetic, sequence and protein level variations. This is a HTM in rice without any IPR (Intellectual Property Rights) infringements and hence can be used in rice breeding as a novel genetic stock by the public funded organizations in the country and elsewhere.

ISSLS PRIZE IN CLINICAL SCIENCE 2017: Is infection the possible initiator of disc disease? An insight from proteomic analysis

STUDY DESIGN

Proteomic and 16S rDNA analysis of disc tissues obtained in vivo.

OBJECTIVE

To address the controversy of infection as an aetiology for disc disorders through protein profiling. There is raging controversy over the presence of bacteria in human lumbar discs in vivo, and if they represent contamination or infection. Proteomics can provide valuable insight by identifying proteins signifying bacterial presence and, also host defence response proteins (HDRPs), which will confirm infection.

METHODS

22 discs (15-disc herniations (DH), 5-degenerate (DD), 2-normal in MRI (NM) were harvested intraoperatively and immediately snap frozen. Samples were pooled into three groups and proteins extracted were analysed with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Post identification, data analysis was performed using Uniprotdb, Pantherdb, Proteome discoverer and STRING network. Authentication for bacterial presence was performed by PCR amplification of 16S rDNA.

RESULTS

LC-MS/MS analysis using Orbitrap showed 1103 proteins in DH group, compared to 394 in NM and 564 in DD. 73 bacterial specific proteins were identified (56 specific for Propionibacterium acnes; 17 for Staphylococcus epidermidis). In addition, 67 infection-specific HDRPs, unique or upregulated, such as Defensin, Lysozyme, Dermcidin, Cathepsin-G, Prolactin-Induced Protein, and Phospholipase-A2, were identified confirming presence of infection. Species-specific primers for P. acnes exhibited amplicons at 946 bp (16S rDNA) and 515 bp (Lipase) confirming presence of P. acnes in both NM discs, 11 of 15 DH discs, and all five DD discs. Bioinformatic search for protein-protein interactions (STRING) documented 169 proteins with close interactions (protein clustering co-efficient 0.7) between host response and degenerative proteins implying that infection may initiate degradation through Ubiquitin C.

CONCLUSION

Our study demonstrates bacterial specific proteins and host defence proteins to infection which strengthen the hypothesis of infection as a possible initiator of disc disease. These results can lead to a paradigm shift in our understanding and management of disc disorders.

Tricuspid Valve Endocarditis

We report a case of isolated native tricuspid valve infective endocarditis caused by Coagulase Negative Staphylococcus in a non-IV drug abuser without structural heart disease. Early diagnosis and prompt initiation of appropriate treatment saved the patient without surgical intervention. The recent trend of Coagulase Negative Staphylococci (CoNS) causing native valve endocarditis (NVE) is reviewed with literature.

Effect of docosahexaenoic acid-enriched fish oil supplementation in pregnant women with Type 2 diabetes on membrane fatty acids and fetal body composition--double-blinded randomized placebo-controlled trial

AIMS

To test if docosahexaenoic acid-enriched fish oil supplementation rectifies red cell membrane lipid anomaly in pregnant women with Type 2 diabetes and their neonates, and alters fetal body composition.

METHODS

Women with Type 2 diabetes (n = 88; 41 fish oil, 47 placebo) and healthy women (n = 85; 45 fish oil, 40 placebo) were supplemented from the first trimester until delivery. Blood fatty acid composition, fetal biometric and neonatal anthropometric measurements were assessed.

RESULTS

A total of 117 women completed the trial. The women with Type 2 diabetes who took fish oil compared with those who received placebo had higher percentage of docosahexaenoic acid in red cell phosphatidylethanolamine in the third trimester (12.0% vs. 8.9%, P = 0.000) and at delivery (10.7% vs. 7.4%, P = 0.001). Similarly, the neonates of the women with Type 2 diabetes supplemented with the fish oil had increased docosahexaenoic acid in the red cell phosphatidylethanolamine (9.2% vs. 7.7%, P = 0.027) and plasma phosphatidylcholine (6.1% vs. 4.7%, P = 0.020). Docosahexaenoic acid-rich fish oil had no effect on the body composition of the fetus and neonates of the women with Type 2 diabetes.

CONCLUSIONS

A daily dose of 600 mg of docosahexaenoic acid was effective in ameliorating red cell membrane docosahexaenoic acid anomaly in pregnant women with Type 2 diabetes and neonates, and in preventing the decline of maternal docosahexaenoic acid during pregnancy. We suggest that the provision of docosahexaenoic acid supplement should be integrated in the antenatal care of pregnant women with Type 2 diabetes.

Quantitative Genetics of Response to Novelty and Other Stimuli by Infant Rhesus Macaques (Macaca mulatta) Across Three Behavioral Assessments

Primate behavior is influenced by both heritable factors and environmental experience during development. Previous studies of rhesus macaques (Macaca mulatta) examined the effects of genetic variation on expressed behavior and related neurobiological traits (heritability and/or genetic association) using a variety of study designs. Most of these prior studies examined genetic effects on the behavior of adults or adolescent rhesus macaques, not in young macaques early in development. To assess environmental and additive genetic variation in behavioral reactivity and response to novelty among infants, we investigated a range of behavioral traits in a large number (N = 428) of pedigreed infants born and housed in large outdoor corrals at the Oregon National Primate Research Center (ONPRC). We recorded the behavior of each subject during a series of brief tests, involving exposure of each infant to a novel environment, to a social threat without the mother present, and to a novel environment with its mother present but sedated. We found significant heritability (h² ) for willingness to move away from the mother and explore a novel environment (h² = 0.25 ± 0.13; P = 0.003). The infants also exhibited a range of heritable behavioral reactions to separation stress or to threat when the mother was not present (h² = 0.23 ± 0.13-0.24 ± 0.15, P < 0.01). We observed no evidence of maternal environmental effects on these traits. Our results extend knowledge of genetic influences on temperament and reactivity in nonhuman primates by demonstrating that several measures of behavioral reactivity among infant rhesus macaques are heritable.

Differential regulation of defense-related gene expression in response to red rot pathogen Colletotrichum falcatum infection in sugarcane

Red rot is a serious disease of sugarcane caused by the fungus Colletotrichum falcatum imposing a considerable economic loss annually in all sugarcane-producing countries. In this study, we analyzed the early resistance response of sugarcane to red rot fungus by comparing the differences between control and inoculated stalk tissues. Differential display reverse transcription polymerase chain reaction (DD-RT-PCR) was employed to identify altered expression of genes in disease-resistant cv Co 93009, in response to pathogen infection. DD-RT-PCR identified 300 differentially expressed transcripts of which 112 were selected for further analysis. Cloning and sequence analysis of the isolated cDNA fragments resulted in functional categorization of these clones into five categories, of which the defense/stress/signaling group was the largest, with clones homologous to genes known to be actively involved in various pathogenesis-related functions in plant species. This group showed overexpression of several transcripts related to ethylene-mediated and jasmonic acid pathway of plant defense mechanisms. Of the 112 expressed sequence tags, validation of expression was carried out for five important genes whose role in plant defense mechanisms is well established. This is the first report of Colletotrichum-mediated gene regulation in sugarcane which has provided a set of candidate genes for detailed molecular dissection of signaling and defense responses in tropical sugarcane during the onset of red rot resistance.

CRHR1 genotypes, neural circuits and the diathesis for anxiety and depression

The corticotrophin-releasing hormone (CRH) system integrates the stress response and is associated with stress-related psychopathology. Previous reports have identified interactions between childhood trauma and sequence variation in the CRH receptor 1 gene (CRHR1) that increase risk for affective disorders. However, the underlying mechanisms that connect variation in CRHR1 to psychopathology are unknown. To explore potential mechanisms, we used a validated rhesus macaque model to investigate association between genetic variation in CRHR1, anxious temperament (AT) and brain metabolic activity. In young rhesus monkeys, AT is analogous to the childhood risk phenotype that predicts the development of human anxiety and depressive disorders. Regional brain metabolism was assessed with (18)F-labeled fluoro-2-deoxyglucose (FDG) positron emission tomography in 236 young, normally reared macaques that were also characterized for AT. We show that single nucleotide polymorphisms (SNPs) affecting exon 6 of CRHR1 influence both AT and metabolic activity in the anterior hippocampus and amygdala, components of the neural circuit underlying AT. We also find evidence for association between SNPs in CRHR1 and metabolism in the intraparietal sulcus and precuneus. These translational data suggest that genetic variation in CRHR1 affects the risk for affective disorders by influencing the function of the neural circuit underlying AT and that differences in gene expression or the protein sequence involving exon 6 may be important. These results suggest that variation in CRHR1 may influence brain function before any childhood adversity and may be a diathesis for the interaction between CRHR1 genotypes and childhood trauma reported to affect human psychopathology.

Enthusiasm and teamwork—the basis for increase in laparoscopic surgery for ectopic pregnancy: an Inner London district hospital experience

Laparoscopic surgery is the gold standard in the surgical management of ectopic pregnancy. It results in lower morbidity, less impact on reproductive health and faster return to normal activity. However, laparoscopic management is not available to all women. Between April 2001 and March 2002 a prospective audit of surgical management of ectopic pregnancy was carried out; 88.7% were performed laparoscopically, most due to concerted consultant input to the care of women with ectopic pregnancy.

Polymorphic microsatellite loci for the common marmoset (Callithrix jacchus) designed using a cost- and time-efficient method

We describe a cost- and time-efficient method for designing new microsatellite markers in any species with substantial genomic DNA sequence data available. Using this technique, we report 14 new polymorphic dinucleotide microsatellite loci isolated from the common marmoset. The relative yield of new polymorphisms was higher with less labor than described in previous marmoset studies. Of 20 loci initially evaluated, 14 were polymorphic and amplified reliably (70% success rate). The number of alleles ranged from 3 to 9 with heterozygosity varying from 0.48 to 0.83.

Granulosa cell survival and proliferation are altered in polycystic ovary syndrome

CONTEXT

Polycystic ovary syndrome (PCOS) represents the most common endocrine abnormality in women of reproductive age. The cause of PCOS remains largely unknown, but studies suggest an intrinsic ovarian abnormality.

OBJECTIVE

The objective of the study was to test our hypothesis that differences in granulosa cell proliferation and apoptosis may underlie abnormalities that affect follicular development.

DESIGN

Granulosa cells were prepared from follicular fluid aspirated from 4- to 8-mm follicles of unstimulated ovaries during routine laparoscopy or laparotomy from women with anovulatory PCOS and those with regular ovulatory cycles.

SETTING

The study was conducted at a university hospital.

PATIENTS

Fourteen women with anovulatory PCOS and nine women with regular ovulatory cycles participated in the study.

MAIN OUTCOME MEASURES

Immunocytochemistry on granulosa cells to investigate apoptotic and proliferation rates, together with real-time RT-PCR to analyze gene expression profiles of apoptotic regulators, was measured.

RESULTS

Significantly lower apoptotic rates were found in granulosa cells from patients with PCOS, compared with women with regular ovulatory cycles (P=0.004). Lower apoptotic rates were associated with decreased levels of the apoptotic effector caspase-3 (P=0.001) and increased levels of the anti-apoptotic survival factor cellular inhibitor of apoptosis proteins-2 in the PCOS group that were coupled to higher proliferation rates (P=0.032). Gene expression profiling confirmed the immunocytochemical findings.

CONCLUSIONS

Our findings indicate that there are significant differences in the rate of cell death and proliferation in granulosa cell populations in PCOS patients. These are associated with decreased expression of apoptotic effectors and increased expression of a cell survival factor. These results provide new insights that may be useful in developing specific therapeutic intervention strategies in PCOS.

Trisomy of chromosome 18 in the baboon (Papio hamadryas anubis)

Trisomy 18 is usually a lethal chromosomal abnormality and is the second most common autosomal trisomy in humans, with an incidence of 1:8000 live births. It is commonly associated with abnormalities of the lower and upper extremities, having the frequency of 95% and 65%, respectively. A newborn female olive baboon (Papio hamadryas anubis) was diagnosed with intrauterine growth retardation and severe arthrogryposis-like congenital joint deformities. Cytogenetic analysis including G-banding and fluorescence in situ hybridization (FISH) revealed that the congenital abnormalities were associated with chromosomal mosaicism for trisomy 18. Genetic analysis with microsatellites from chromosome 18 confirmed the maternal origin of the extra chromosome 18. This is the first report of trisomy 18 in the baboon, which may be a promising animal model of human disease.

Tissue-specific expression and drought responsiveness of cell-wall invertase genes of rice at flowering

Drought stress near heading reduces grain yield in rice cultivars by inhibiting processes such as anther dehiscence and panicle exsertion. Because cell-wall invertases play an important role in carbon allocation to developing organs, we examined the tissue-specific expression and drought sensitivity of the corresponding genes (OsCIN1-9) at heading in the widely grown cultivar IR64. OsCIN1-5,8 were expressed to varying degrees in flag leaf, panicle, anthers and peduncle at 1 day before heading (1 DBH). When water was withheld for 2 days starting 3 DBH, anthesis and peduncle elongation were halted. At the same time, transcript levels for OsCIN1-5,8 genes were all markedly down-regulated in anthers and/or peduncles but were not affected in flag leaves. Re-watering allowed anthesis and peduncle elongation to proceed and restored expression of OsCIN1-5,8. We conclude that cell-wall invertase genes, as a class, respond rapidly to water deficit in anthers and peduncles and through a reduction in sink strength help to coordinate a delay in anthesis and heading. By contrast, vacuolar invertase OsVIN2 was up-regulated by drought stress in flag leaves, panicles, anthers and peduncles. Although OsCIN1-3,5,8 were active in the peduncle, only OsCIN2 was expressed strongly and preferentially at the base, where cell division and cell elongation occur. OsCIN2 was expressed principally in the primary and secondary vascular systems, consistent with a role in diverting sucrose from the phloem to the dividing and expanding cells of the peduncle, whereas the less abundant OsCIN1,3,5,8 transcripts were found principally in parenchyma cells. The OsCIN2 transcript levels in the base were highest at 1 DBH, when rapid peduncle elongation began. Drought stress halted peduncle elongation and reduced OsCIN2 transcript level to 8% of the control level. On re-watering, peduncle elongation was restored and OsCIN2 transcript level recovered to 24% of the control. The abscisic acid (ABA) level of peduncles increased 7-fold on drought stress and returned to the control level on re-watering. Detached peduncles floated on water elongated little and lost all OsCIN2 transcripts, but on 50-100 microM GA3 they elongated rapidly and maintained high OsCIN2 transcript levels. ABA antagonized both peduncle elongation and maintenance of OsCIN2 transcript levels. We conclude that this antagonism is a potential intervention point for breeding strategies directed at enhancing panicle exsertion during or after drought stress at heading.

Effect of water-soluble fraction of cigarette smoke on human aortic endothelial cells--a proteomic approach

Proteomic analysis is an important investigative tool used to systematically explore cellular proteins that are responsive to adverse environmental challenges. Tobacco smoking is the second major cause of death in the world. In this study, we utilized two-dimensional electrophoresis (2-DE) and mass spectrometry (MS) technologies to explore protein changes in human aortic endothelial cells (HAECs) in response to cigarette smoke extracts (CSE). Among 389 individual proteins resolved using 2-DE, 43 had a 2- to 3-fold change in levels as measured by spot intensity and 32 had more than a 3-fold change. Sixteen of the 32 spots with sufficient amount of proteins were excised for identification by performing matrix-assisted laser desorption/ionization (MALDI)-MS analysis. Using a peptide mass fingerprinting (PMF) to search the nrNCBI database, we identified all these 16 proteins, which were either increased (n = 9) or decreased (n = 7) after CSE treatment. All these proteins have known functions, however, none have been reported to be altered after CSE treatment. The findings from our study suggest that utilizing a systemic investigative tool, such as the proteomic approach using 2-DE, may play an important role in discovering novel molecular mechanisms for cigarette smoking-induced pathological changes. Further investigation following the systemic discoveries must be further examined as they may potentially lead to new therapeutic approaches to smoking-induced diseases - a health issue affecting everyone in the world.

Human cytomegalovirus causes endothelial injury through the ataxia telangiectasia mutant and p53 DNA damage signaling pathways

Atherosclerosis is the leading cause of death in the United States, and human cytomegalovirus (HCMV), a member of the herpes virus family, may play a role in the development of the disease. We previously showed that HCMV regulated endothelial apoptosis. In this study, we investigated the induction of apoptosis and signal transduction pathways regulating this process in HCMV-infected endothelial cells. As observed previously, HCMV induced a typical cytopathic effect in human aortic endothelial cells (HAECs), ie, the formation of single nucleated or multinucleated giant cells. Although infected HAECs were resistant to apoptosis at earlier stages of infection, they became apoptotic with prolonged infection as demonstrated by positive staining using terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL). This apoptotic process was mediated by the caspase-dependent mitochondrial apoptotic pathway as indicated by increased expression and cleavage of caspases 3 and 9 as well as increased expressions of pro-apoptotic molecules Bax and Bak. Blocking caspases 3 or 9 significantly inhibited the HCMV-induced apoptosis. Further exploration of the upstream pathway demonstrated upregulation of the tumor suppressor p53 gene and activation of the ataxia telangiectasia mutant (ATM) pathway in the infected cells. Blocking p53 inhibited HCMV-stimulated Bax and Bak expression as well as caspase-3 activation and blocking the ATM pathway inhibited HCMV-stimulated p53 activation. Although early infection may render cells antiapoptotic, prolonged infection, however, induced endothelial apoptosis through ATM and p53-dependent activation of the mitochondrial death pathway. This proapoptotic effect may be relevant to endothelial dysfunction and HCMV-associated vascular diseases.

Effect of chronic glutathione deficiency on rat lung mitochondrial function

The effect of chronic glutathione deficiency on lung mitochondrial energy production using buthionine sulphoximine (BSO) as a depletor has been investigated. Prolonged depletion of mitochondrial glutathione produced an imbalance in the antioxidant defence and resulted in lipid peroxidation, which, in turn, damages the membranous structure, leading to the inactivation of inner membrane enzymes, matrix-bound enzymes and mitochondrial cytochrome content. Altered activities of energy-linked enzymes and electron transport resulted in the decreased rate of ADP-stimulated oxygen uptake, respiratory coupling ratio and ATP synthesis.

Buthionine sulfoximine-induced glutathione depletion. Its effect on antioxidants, lipid peroxidation and calcium homeostasis in the lung

The administration of buthionine sulfoximine (BSO), an irreversible inhibitor of gamma-glutamylcysteine synthetase, produces glutathione (GSH) depletion in tumors, making them sensitive to drugs and radiation. During the process, it also depletes GSH from normal tissues. Certain tumors require frequent doses of BSO for several days to produce GSH depletion. In this study, we determined that this chronic GSH-deficient condition lowers the antioxidant defense of the lung by diminishing the activities of superoxide dismutase, catalase, and glutathione peroxidase and the levels of ascorbic acid and alpha-tocopherol. Impaired antioxidant defense leads to enhanced lipid peroxidation, as indicated by increased levels of thiobarbituric acid reactive substances and conjugated dienes. The alteration of protein thiols by lipid peroxidation, is responsible for altered Ca2+ homeostasis, which, in turn, leads to cell injury. Cell injury was confirmed by elevated activities of angiotensin converting enzyme and lactate dehydrogenase, increased levels of protein and lactate, and histopathological changes.