Breeding histories and selection criteria for oilseed rape in Europe and China identified by genome wide pedigree dissection

Selection breeding has played a key role in the improvement of seed yield and quality in oilseed rape (Brassica napus L.). We genotyped Tapidor (European), Ningyou7 (Chinese) and their progenitors with the Brassica 60 K Illumina Infinium SNP array and mapped a total of 29,347 SNP markers onto the reference genome of Darmor-bzh. Identity by descent (IBD) refers to a haplotype segment of a chromosome inherited from a shared common ancestor. IBDs identified on the C subgenome were larger than those on the A subgenome within both the Tapidor and Ningyou7 pedigrees. IBD number and length were greater in the Ningyou7 pedigree than in the Tapidor pedigree. Seventy nine QTLs for flowering time, seed quality and root morphology traits were identified in the IBDs of Tapidor and Ningyou7. Many more candidate genes had been selected within the Ningyou7 pedigree than within the Tapidor pedigree. These results highlight differences in the transfer of favorable gene clusters controlling key traits during selection breeding in Europe and China

Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast

Abstract Background In eukaryotic organisms, DNA is packaged into chromatin structure, where most of DNA is wrapped into nucleosomes. DNA compaction and nucleosome positioning have clear functional implications, since they modulate the accessibility of genomic regions to regulatory proteins. Despite the intensive research effort focused in this area, the rules defining nucleosome positioning and the location of DNA regulatory regions still remain elusive. Results Naked (histone-free) and nucleosomal DNA from yeast were digested by microccocal nuclease (MNase) and sequenced genome-wide. MNase cutting preferences were determined for both naked and nucleosomal DNAs. Integration of their sequencing profiles with DNA conformational descriptors derived from atomistic molecular dynamic simulations enabled us to extract the physical properties of DNA on a genomic scale and to correlate them with chromatin structure and gene regulation. The local structure of DNA around regulatory regions was found to be unusually flexible and to display a unique pattern of nucleosome positioning. Ab initio physical descriptors derived from molecular dynamics were used to develop a computational method that accurately predicts nucleosome enriched and depleted regions. Conclusions Our experimental and computational analyses jointly demonstrate a clear correlation between sequence-dependent physical properties of naked DNA and regulatory signals in the chromatin structure. These results demonstrate that nucleosome positioning around TSS (Transcription Start Site) and TTS (Transcription Termination Site) (at least in yeast) is strongly dependent on DNA physical properties, which can define a basal regulatory mechanism of gene expression

Maternal health interventions in resource limited countries: a systematic review of packages, impacts and factors for change

The burden of maternal mortality in resource limited countries is still huge despite being at the top of the global public health agenda for over the last 20 years. We systematically reviewed the impacts of interventions on maternal health and factors for change in these countries. A systematic review was carried out using the guidelines for Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). Articles published in the English language reporting on implementation of interventions, their impacts and underlying factors for maternal health in resource limited countries in the past 23 years were searched from PubMed, Popline, African Index Medicus, internet sources including reproductive health gateway and Google, hand-searching, reference lists and grey literature. Out of a total of 5084 articles resulting from the search only 58 qualified for systematic review. Programs integrating multiple interventions were more likely to have significant positive impacts on maternal outcomes. Training in emergency obstetric care (EmOC), placement of care providers, refurbishment of existing health facility infrastructure and improved supply of drugs, consumables and equipment for obstetric care were the most frequent interventions integrated in 52%-65% of all 54 reviewed programs. Statistically significant reduction of maternal mortality ratio and case fatality rate were reported in 55% and 40% of the programs respectively. Births in EmOC facilities and caesarean section rates increased significantly in 71%-75% of programs using these indicators. Insufficient implementation of evidence-based interventions in resources limited countries was closely linked to a lack of national resources, leadership skills and end-users factors. This article presents a list of evidenced-based packages of interventions for maternal health, their impacts and factors for change in resource limited countries. It indicates that no single magic bullet intervention exists for reduction of maternal mortality and that all interventional programs should be integrated in order to bring significant changes. State leaders and key actors in the health sectors in these countries and the international community are proposed to translate the lessons learnt into actions and intensify efforts in order to achieve the goals set for maternal health

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

SOME SERUM BIOCHEMICAL CONSTITUENTS OF MARES DURING DIFFERENT PHASES OF REPRODUCTIVE CYCLE

Serum glucose, total proteins, calcium and inorganic phosphorus were determined in estrual, pregnant, infertile and regular breeder mares, each group comprising of 10 animals. The mares were grouped on the basis of rectal examination, history and records. There was a significant (P<0.05) difference in the serum glucose levels between the pregnant and estrual mares, pregnant and regular breeder mares, infertile and regular breeder mares and between infertile and estrual mares. The highest values of serum glucose were recorded in regular breeder mares, whereas the lowest values were recorded in infertile mares. The highest values for total proteins were recorded in regular breeder mares and the lowest in pregnant mares, difference being significant (P<0.05) between the pregnant and estrual and pregnant and regular breeder mares. The highest values of serum calcium were recorded in estrual mares and lowest for regular breeder mares. There was a significant (P<0.05) difference between the estrual and pregnant mares, estrual and infertile mares and between estrual and regular breeder mares. The highest values of serum inorganic phosphorus were recorded for regular breeder mares whereas the lowest values were recorded in pregnant mares. The analysis of data indicated non significant (P>0.05) difference in the serum phosphorus levels among all the groups of mares