Energy balance drives diurnal and nocturnal brain transcriptome rhythms.

Plasticity in daily timing of activity has been observed in many species, yet the underlying mechanisms driving nocturnality and diurnality are unknown. By regulating how much wheel-running activity will be rewarded with a food pellet, we can manipulate energy balance and switch mice to be nocturnal or diurnal. Here, we present the rhythmic transcriptome of 21 tissues, including 17 brain regions, sampled every 4 h over a 24-h period from nocturnal and diurnal male CBA/CaJ mice. Rhythmic gene expression across tissues comprised different sets of genes with minimal overlap between nocturnal and diurnal mice. We show that non-clock genes in the suprachiasmatic nucleus (SCN) change, and the habenula was most affected. Our results indicate that adaptive flexibility in daily timing of behavior is supported by gene expression dynamics in many tissues and brain regions, especially in the habenula, which suggests a crucial role for the observed nocturnal-diurnal switch.

Diurnal transcriptome landscape of a multi-tissue response to time-restricted feeding in mammals.

Time-restricted feeding (TRF) is an emerging behavioral nutrition intervention that involves a daily cycle of feeding and fasting. In both animals and humans, TRF has pleiotropic health benefits that arise from multiple organ systems, yet the molecular basis of TRF-mediated benefits is not well understood. Here, we subjected mice to isocaloric ad libitum feeding (ALF) or TRF of a western diet and examined gene expression changes in samples taken from 22 organs and brain regions collected every 2 h over a 24-h period. We discovered that TRF profoundly impacts gene expression. Nearly 80% of all genes show differential expression or rhythmicity under TRF in at least one tissue. Functional annotation of these changes revealed tissue- and pathway-specific impacts of TRF. These findings and resources provide a critical foundation for future mechanistic studies and will help to guide human time-restricted eating (TRE) interventions to treat various disease conditions with or without pharmacotherapies.

Co-located quantitative trait loci mediate resistance to Agrobacterium tumefaciens, Phytophthora cinnamomi, and P. pini in Juglans microcarpa × J. regia hybrids.

Soil-borne plant pathogens represent a serious threat that undermines commercial walnut (Juglans regia) production worldwide. Crown gall, caused by Agrobacterium tumefaciens, and Phytophthora root and crown rots, caused by various Phytophthora spp., are among the most devastating walnut soil-borne diseases. A recognized strategy to combat soil-borne diseases is adoption of resistant rootstocks. Here, resistance to A. tumefaciens, P. cinnamomi, and P. pini is mapped in the genome of Juglans microcarpa, a North American wild relative of cultivated walnut. Half-sib J. microcarpa mother trees DJUG 31.01 and DJUG 31.09 were crossed with J. regia cv. Serr, producing 353 and 400 hybrids, respectively. Clonally propagated hybrids were genotyped by sequencing to construct genetic maps for the two populations and challenged with the three pathogens. Resistance to each of the three pathogens was mapped as a major QTL on the long arm of J. microcarpa chromosome 4D and was associated with the same haplotype, designated as haplotype b, raising the possibility that the two mother trees were heterozygous for a single Mendelian gene conferring resistance to all three pathogens. The deployment of this haplotype in rootstock breeding will facilitate breeding of a walnut rootstock resistant to both crown gall and Phytophthora root and crown rots.

Genome-wide introgression from a bread wheat × Lophopyrum elongatum amphiploid into wheat.

KEY MESSAGE: We introgressed wheatgrass germplasm from the octoploid amphiploid Triticum aestivum× Lophopyrum elongatum into wheat by manipulating the wheat Ph1 gene and discovered and characterized 130 introgression lines harboring single or, in various combinations, complete and recombined L. elongatum chromosomes. Diploid wheatgrass Lophopyrum elongatum (genomes EE) possesses valuable traits for wheat genetics and breeding. We evaluated several strategies for introgression of this germplasm into wheat. To detect it, we developed and validated multiplexed sets of Sequenom MassARRAY single nucleotide polymorphism (SNP) markers, which differentiated disomic and monosomic L. elongatum chromosomes from wheat chromosomes. We identified 130 introgression lines (ILs), which harbored 108 complete and 89 recombined L. elongatum chromosomes. Of the latter, 59 chromosomes were recombined by one or more crossovers and 30 were involved in centromeric (Robertsonian) translocations or were telocentric. To identify wheat chromosomes substituted for or recombined with L. elongatum chromosomes, we genotyped the ILs with the wheat 90-K Infinium SNP array. We found that most of the wheat 90-K probes correctly detected their targets in the L. elongatum genome and showed that some wheat SNPs are ancient and had originated prior to the divergence of the wheat and L. elongatum lineages. Of the 130 ILs, 52% were homozygous for Ph1 deletion and thus are staged to be recombined further. We failed to detect in the L. elongatum genome the 4/5 reciprocal translocation that has been reported in Thinopyrum bessarabicum and several other Triticeae genomes.

Aegilops tauschii Genome Sequence: A Framework for Meta-analysis of Wheat QTLs.

Numerous quantitative trait loci (QTL) have been mapped in tetraploid and hexaploid wheat and wheat relatives, mostly with simple sequence repeat (SSR) or single nucleotide polymorphism (SNP) markers. To conduct meta-analysis of QTL requires projecting them onto a common genomic framework, either a consensus genetic map or genomic sequence. The latter strategy is pursued here. Of 774 QTL mapped in wheat and wheat relatives found in the literature, 585 (75.6%) were successfully projected onto the Aegilops tauschii pseudomolecules. QTL mapped with SNP markers were more successfully projected (92.2%) than those mapped with SSR markers (66.2%). The QTL were not distributed homogeneously along chromosome arms. Their frequencies increased in the proximal-to-distal direction but declined in the most distal regions and were weakly correlated with recombination rates along the chromosome arms. Databases for projected SSR markers and QTL were constructed and incorporated into the Ae. tauschii JBrowse. To facilitate meta-QTL analysis, eight clusters of QTL were used to estimate standard deviations ([Formula: see text]) of independently mapped QTL projected onto the Ae. tauschii genome sequence. The standard deviations [Formula: see text] were modeled as an exponential decay function of recombination rates along the Ae. tauschii chromosomes. We implemented four hypothesis tests for determining the membership of query QTL. The hypothesis tests and estimation procedure for [Formula: see text] were implemented in a web portal for meta-analysis of projected QTL. Twenty-one QTL for Fusarium head blight resistance mapped on wheat chromosomes 3A, 3B, and 3D were analyzed to illustrate the use of the portal for meta-QTL analyses.

Structural variation and rates of genome evolution in the grass family seen through comparison of sequences of genomes greatly differing in size.

Homology was searched with genes annotated in the Aegilops tauschii pseudomolecules against genes annotated in the pseudomolecules of tetraploid wild emmer wheat, Brachypodium distachyon, sorghum and rice. Similar searches were performed with genes annotated in the rice pseudomolecules. Matrices of collinear genes and rearrangements in their order were constructed. Optical BioNano genome maps were constructed and used to validate rearrangements unique to the wild emmer and Ae. tauschii genomes. Most common rearrangements were short paracentric inversions and short intrachromosomal translocations. Intrachromosomal translocations outnumbered segmental intrachromosomal duplications. The densities of paracentric inversion lengths were approximated by exponential distributions in all six genomes. Densities of collinear genes along the Ae. tauschii chromosomes were highly correlated with meiotic recombination rates but those of rearrangements were not, suggesting different causes of the erosion of gene collinearity and evolution of major chromosome rearrangements. Frequent rearrangements sharing breakpoints suggested that chromosomes have been rearranged recurrently at some sites. The distal 4 Mb of the short arms of rice chromosomes Os11 and Os12 and corresponding regions in the sorghum, B. distachyon and Triticeae genomes contain clusters of interstitial translocations including from 1 to 7 collinear genes. The rates of acquisition of major rearrangements were greater in the large wild emmer wheat and Ae. tauschii genomes than in the lineage preceding their divergence or in the B. distachyon, rice and sorghum lineages. It is suggested that synergy between large quantities of dynamic transposable elements and annual growth habit have been the primary causes of the fast evolution of the Triticeae genomes.

A High-Density Genetic Map of Wild Emmer Wheat from the Karaca Dag Region Provides New Evidence on the Structure and Evolution of Wheat Chromosomes.

Wild emmer (Triticum turgidum ssp. dicoccoides) is a progenitor of all cultivated wheat grown today. It has been hypothesized that emmer was domesticated in the Karaca Dag region in southeastern Turkey. A total of 445 recombinant inbred lines of T. turgidum ssp. durum cv. 'Langdon' x wild emmer accession PI 428082 from this region was developed and genotyped with the Illumina 90K single nucleotide polymorphism Infinium assay. A genetic map comprising 2,650 segregating markers was constructed. The order of the segregating markers and an additional 8,264 co-segregating markers in the Aegilops tauschii reference genome sequence was used to compare synteny of the tetraploid wheat with the Brachypodium distachyon, rice, and sorghum. These comparisons revealed the presence of 15 structural chromosome rearrangements, in addition to the already known 4A-5A-7B rearrangements. The most common type was an intra-chromosomal translocation in which the translocated segment was short and was translocated only a short distance along the chromosome. A large reciprocal translocation, one small non-reciprocal translocation, and three large and one small paracentric inversions were also discovered. The use of inversions for a phylogeny reconstruction in the Triticum-Aegilops alliance was illustrated. The genetic map was inconsistent with the current model of evolution of the rearranged chromosomes 4A-5A-7B. Genetic diversity in the rearranged chromosome 4A showed that the rearrangements might have been contemporary with wild emmer speciation. A selective sweep was found in the centromeric region of chromosome 4A in Karaca Dag wild emmer but not in 4A of T. aestivum. The absence of diversity from a large portion of chromosome 4A of wild emmer, believed to be ancestral to all domesticated wheat, is puzzling.

Genome sequence of the progenitor of the wheat D genome Aegilops tauschii.

Aegilops tauschii is the diploid progenitor of the D genome of hexaploid wheat (Triticum aestivum, genomes AABBDD) and an important genetic resource for wheat. The large size and highly repetitive nature of the Ae. tauschii genome has until now precluded the development of a reference-quality genome sequence. Here we use an array of advanced technologies, including ordered-clone genome sequencing, whole-genome shotgun sequencing, and BioNano optical genome mapping, to generate a reference-quality genome sequence for Ae. tauschii ssp. strangulata accession AL8/78, which is closely related to the wheat D genome. We show that compared to other sequenced plant genomes, including a much larger conifer genome, the Ae. tauschii genome contains unprecedented amounts of very similar repeated sequences. Our genome comparisons reveal that the Ae. tauschii genome has a greater number of dispersed duplicated genes than other sequenced genomes and its chromosomes have been structurally evolving an order of magnitude faster than those of other grass genomes. The decay of colinearity with other grass genomes correlates with recombination rates along chromosomes. We propose that the vast amounts of very similar repeated sequences cause frequent errors in recombination and lead to gene duplications and structural chromosome changes that drive fast genome evolution.

Urinary 8-hydroxydeoxyguanosine as a marker of oxidative stress induced genetic toxicity in oral cancer patients.

CONTEXT: Recently, non-communicable diseases have snatched the lead from infectious diseases in causing mortality. Of these, oral cancer accounts for a significant proportion of deaths. Every year in India significant percentage of newly diagnosed malignancy is oral cancer attributed to various reasons. AIMS: The aim of this study was to assess the extent of oxidative stress and its effect on modification of DNA by urinary nucleoside 8-hydroxy-2'-deoxyguanosine (8-OHdG) levels in oral cancer subjects. To see the relationship between the nucleoside 8-OHdG and antioxidant capacity ferric reducing ability plasma (FRAP) in oral cancer subjects. SETTINGS AND DESIGN: Case-control study included three groups with 60 volunteers, who were divided into 30 controls, and equal number of clinically diagnosed oral cancer male patients: (Subdivided into newly diagnosed [n = 15] and 1-year treatment follow-up oral cancer subjects [n = 15]). MATERIALS AND METHODS: A random urine sample was used for analysis of 8-OHdG concentration. Serum triglycerides, lipid peroxidation, protein thiols, and FRAP assay were performed by spectrophotometric technique. STATISTICAL ANALYSIS USED: Student's t-test and one-way analysis of variance were performed for group comparison and Pearson's correlation analysis were used. A P < 0.05 was considered the optimum level of significance. RESULTS: The urinary 8-OHdG and serum malondialdehyde levels were significantly elevated in newly diagnosed oral cancer subjects in their 1-year treatment compared to the control group (P < 0.05). A significant correlation was observed between urinary 8-OHdG and FRAP in both groups of oral cancer subjects. CONCLUSIONS: Urinary 8-OHdG can be a useful diagnostic marker of oxidative DNA damage in oral cancer subjects.

STRUCTURE PLOT: a program for drawing elegant STRUCTURE bar plots in user friendly interface.

BACKGROUND: Understanding structure of the population is one of the major objective of many genetic studies. The program STRUCTURE is commonly used to infer population structure using multi-locus genotype data. However, a tool with graphical-user interface is currently not available to visualize STRUCTURE bar plots. RESULTS: We introduce STRUCTURE PLOT, a program for drawing STRUCTURE bar plots. The program generates publication ready, aesthetic STRUCTURE bar plots by using individual Q matrix from STRUCTURE or CLUMPP output. The program is very simple to use and includes variety of options like sorting bar by original order or by K, and selection of colors from R colors or RColorBrewer palette. Individual or population labels can be printed below or above the plot in any angle. Size of the graph and label can be defined, and option is provided to save plot in variety of picture formats in user defined resolution. CONCLUSION: The program is implemented as a web application for online users and also as a standalone shiny application. Web application is compatible to majority of leading web browsers and standalone version can be launched using a simple R command. The program can be freely accessed at http://btismysore.in/strplot.

Biosensors in clinical chemistry: An overview.

Biosensors are small devices that employ biological/biochemical reactions for detecting target analytes. Basically, the device consists of a biocatalyst and a transducer. The biocatalyst may be a cell, tissue, enzyme or even an oligonucleotide. The transducers are mainly amperometric, potentiometric or optical. The classification of biosensors is based on (a) the nature of the recognition event or (b) the intimacy between the biocatalyst and the transducer. Bioaffinity and biocatalytic devices are examples for the former and the first, whereas second and third generation instruments are examples for the latter. Cell-based biosensors utilizing immobilized cells, tissues as also enzyme immunosensors and DNA biosensors find variegated uses in diagnostics. Enzyme nanoparticle-based biosensors make use of small particles in the nanometer scale and are currently making a mark in laboratory medicine. Nanotechnology can help in optimizing the diagnostic biochips, which would facilitate sensitive, rapid, accurate and precise bedside monitoring. Biosensors render themselves as capable diagnostic tools as they meet most of the above-mentioned criteria.

Diagnostic utility of heat stable alkaline phosphatase in hypertensive disorders of pregnancy.

BACKGROUND: Hypertensive disorders in pregnancy (HDP) complicate 3-10% of all pregnancies. Though there are several biochemical parameters which aid in predicting hypertension of pregnancy, human placental alkaline phosphatase (PLAP), synthesized in placenta during pregnancy by placental syncytiotrophoblast, assumes diagnostic relevance. The purpose of this study was to compare the total alkaline phosphatase (ALP) and heat stable placental alkaline phosphatase (PLAP) levels in the serum of normotensive and hypertensive disorders of pregnancy and to evaluate the clinical utility of ALP and PLAP as a reliable, sensitive, specific and economical biochemical marker of HDP. MATERIALS AND METHODS: This was a case control study, carried out on pregnant women with hypertension, of south Indian population. Study included pregnant women, 60 patients with hypertension and 60 controls. Biochemical assays were carried out by the IFCC approved procedures based on spectrophotometric method and using fully automated random access chemistry analyser. Data was compared by using student t-test. ROC was drawn to find out optimum cut off for ALP, PLAP and PLAP/ALP ratio in HDP. Pearson's correlation was performed to ascertain the association among markers. RESULTS: Serum total ALP, PLAP and PLAP/ALP ratio levels were significantly higher in hypertensive pregnant women when compared to controls (p<0.05). There was significant correlation among ALP, PLAP and DBP. ROC analysis of ALP (169.5), PLAP (69) and PLAP/ALP (0.44) ratios showed optimum cut-offs in diagnosis of hypertension in pregnancy. CONCLUSION: Serum heat stable ALP isoenzyme and PLAP/ALP ratio could be useful adjuvant markers in diagnosis of HDP in association with other relevant and economically viable biochemical tests.

The prospect of serum magnesium and an electrolyte panel as an adjuvant cardiac biomarker in the management of acute myocardial infarction.

BACKGROUND: Ischemic heart disease accounts 12.2% deaths worldwide. Serum magnesium (Mg+) status is often ignored in Acute Myocardial Infarction (AMI). Studies showed alterations in the levels of serum electrolytes including magnesium in AMI. AIM: To evaluate serum Mg+ and other electrolytes as adjuvant markers in the diagnosis of AMI. DESIGN AND SETTINGS: Case control study was conducted in South Indian male population with AMI within six hours of onset of symptoms. PATIENTS AND METHODS: Study includes sixty patients with AMI and 100 controls. Serum electrolytes were estimated using electrolyte analyzer. Data were compared by using student't' test. ROC was drawn to find out optimum cutoff for diagnosing AMI. Pearson's correlation was done to see the association among the markers. RESULTS: Serum Ca, Mg, K and Na electrolytes were significantly lower ('p'<0.001) in AMI. Ca:Mg, K:Mg, and Na:K ratios were significantly higher when compared to controls ('p'<0.001). There was significant correlation of serum Mg levels with other cardiac markers (Total CK, CK-Mb, Troponin -T) of AMI ('p' <0.05).ROC analysis of Na:Mg (40.9), Ca:Mg (3.43) and K:Mg (2.74) ratios showed optimum cutoffs in diagnosis of AMI. CONCLUSION: Serum Mg, Ca:mg, K:mg and Na:K ratios could be useful adjuvant markers in diagnosis of AMI.

Planning an objective and need based curriculum: the logistics with reference to the undergraduate medical education in biochemistry.

PURPOSE: The medical education is recently being transformed into several domains in order to adapt to the need and the value based academics which is required for the quality doctors who serve the community. Presently, the biochemistry curricula for the graduate students of medicine have been questioned by as many experts, because of their multiple lacunae. In this review, we would like to highlight the scenario which is related to the existing biochemistry curricula for graduate medical students, which have been followed in several medical schools and universities and we also hope to share our ideas for implementing objective and pragmatic curricula. Evidence based research, wherein the articles which are related to innovative teaching-learning tools are collected and the pros and cons which are related to the different methods analyzed in biochemistry point of view. CONCLUSION: Rapid changes in the content of the curriculum may not be required, but a gradual introduction of the novel approach and the methods of teaching biochemistry can be adopted into the curriculum.