Are shed hair genomes the most effective noninvasive resource for estimating relationships in the wild?

1. Knowledge of relationships in wild populations is critical for better understanding mating systems and inbreeding scenarios to inform conservation strategies for endangered species. To delineate pedigrees in wild populations, study genetic connectivity, study genotype‐phenotype associations, trace individuals, or track wildlife trade, many identified individuals need to be genotyped at thousands of loci, mostly from noninvasive samples. This requires us to (a) identify the most common noninvasive sample available from identified individuals, (b) assess the ability to acquire genome‐wide data from such samples, and (c) evaluate the quality of such genome‐wide data, and its ability to reconstruct relationships between animals within a population.
2. We followed identified individuals from a wild endangered tiger population and found that shed hair samples were the most common compared to scat samples, opportunistically found carcasses, and opportunistic invasive samples. We extracted DNA from these samples, prepared whole genome sequencing libraries, and sequenced genomes from these.
3. Whole genome sequencing methods resulted in between 25%–98% of the genome sequenced for five such samples. Exploratory population genetic analyses revealed that these data were free of holistic biases and could recover expected population structure and relatedness. Mitochondrial genomes recovered matrilineages in accordance with long‐term monitoring data. Even with just five samples, we were able to uncover the matrilineage for three individuals with unknown ancestry.
4. In summary, we demonstrated that noninvasive shed hair samples yield adequate quality and quantity of DNA in conjunction with sensitive library preparation methods, and provide reliable data from hundreds of thousands of SNPs across the genome. This makes shed hair an ideal noninvasive resource for studying individual‐based genetics of elusive endangered species in the wild.

     

Influence of segment width on plan quality for volumetric modulated arc based stereotactic body radiotherapy

Aim

To study the influence of segment width on plan quality for volumetric modulated arc based stereotactic body radiotherapy.

Background

The redundancy of modulation for regularly shaped small volume tumors results in creation of many small segments and an increase of monitor units, with a consequent prolongation of treatment and uncertainty in treatment delivery.

Materials and methods

Six cases each in lung, abdomen and liver were taken for the study. For each case, three VMAT SBRT plans were generated with different penalties on minimum segment width of 0.5, 1.0 and 1.5 cm. A comparison was made on the metrics of dose volume histogram, dosimetric indices, monitor units (MUs) and delivery accuracy.

Results

The mean reduction of total MUs when compared with 0.5 cm plan was observed as 12.7 ± 6.0% and 17.5 ± 7.2% for 1.0 cm and 1.5 cm of minimum segment width, respectively. The p value showed a significant degradation in dosimetric indices for 1.5 cm plans when compared with 0.5 cm and 1.0 cm plans. The average deviation of measured dose with TPS calculated was 3.0 ± 1.1%, 2.1 ± 0.84% and 1.8 ± 0.9% for 0.5, 1.0 and 1.5 cm, respectively. The calculated gamma index with pass criteria of 2% dose difference and 2 mm distance to agreement was 95.9 ± 2.8%, 96.5 ± 2.6% and 97.8 ± 1.6% as calculated for 0.5, 1.0 and 1.5 cm of penalties, respectively. In view of the trade off between delivery efficiency and plan quality, 1 cm minimum segment width plans showed an improvement.

Conclusions

VMAT SBRT plans with increased optimal value of minimum segment width showed better plan quality and delivery efficiency for stereotactic body radiotherapy.     

Estimation of Design and Genetic Components of Variance in Double Cross Mating Designs

The present paper deals with the estimation of design and genetic components of variance based on full double crosses and partial tetra-allel crosses. We have presented the explicit experissions for the symmetric sums estimators of design components of variance based on Hinkelmann's model. Consequently we have also presented explicitly the genetic components of variance based on full double crosses and partial tetra-allel crosses. The procedure is also illustrated with the help of a hypothetical data.     

A Note on Estimation of Several Missing Values in Two Way Classified Data with Many Observations Per Cell

In this paper an attempt has been made to reduce the computational complexities involved in estimation of several missing values. As a result it has been shown that one can estimate m missing values by developing only k (≤m) linear equations, where m and k are respectively the number of missing values and missing cells. The procedure is also illustrated with the help of a numerical example.     

Radiation resistance in Schizosaccharomyces pombe

The fission yeast Schizosaccharomyces pombe serves as an excellent alternative and complementary model system for the analysis of genes and gene products involved in DNA repair. This brief review outlines the advantages of S. pombe and describes the radiation-sensitive mutants available for the analysis of DNA repair and recombination mechanisms in this organism. The progress in the cloning and characterization of representative genes is also described.     

In silico genome analysis and drug efficacy test of influenza A virus (H1N1) 2009

The H1N1 2009 virus is pandemic in many countries. The genome of this virus contains eight segments. Among the eight segments maximum numbers of mutation occur at the segment 1 and segment 4 which codes for PB2 subunit and hemagglutinin (HA) and less number of mutations occur in segment 6 which codes for neuraminidase (NA) protein. Neuraminidase (NA) inhibitors (Oseltamivir and Zanamivir) are presently used as an anti-flu drugs. In the present study, the in silico efficacy of different drugs was tested against the swine flu virus. 3D structures of neuraminidase (NA) proteins of H1N1 2009 were generated using Geno3D. The 3D structure of H1N1 1918 was downloaded from PDB. Interaction study was done using Arguslab 4 and PyMol view. Oseltamivir and Zanamivir have good number of interactions with H1N1 2009 virus and the scoring function also support to this result. When compared with the 1918 H1N1 viral protein, 2009 H1N1 NA protein shows more number of interaction and good scoring function. The RMSD value of before and after docking are found to be same at 0.04A° for both the drugs. The force field energy of NA protein 2009 was found to be −15603.529 KJ/mol before docking. The force field energy was found to be decreased after docking at −17620.740 KJ/mol with Tamiflu and −17652.242 KJ/mol with Zanamivir. The number of interaction and scoring function shows that Oseltamivir and Zanamivir will be able to effectively control the present pandemic H1N1 virus 2009.     

Prostate apoptosis response-4 and tumor suppression: it’s not just about apoptosis anymore

The tumor suppressor prostate apoptosis response-4 (Par-4) has recently turned ‘twenty-five’. Beyond its indisputable role as an apoptosis inducer, an increasing and sometimes bewildering, new roles for Par-4 are being reported. These roles include its ability to regulate autophagy, senescence, and metastasis. This growing range of responses to Par-4 is reflected by our increasing understanding of the various mechanisms through which Par-4 can function. In this review, we summarize the existing knowledge on Par-4 tumor suppressive mechanisms, and discuss how the interaction of Par-4 with different regulators influence cell fate. This review also highlights the new secretory pathway that has emerged and the likely discussion on its clinical implications.Subject terms: Tumour-suppressor proteins, Apoptosis, Stress signalling, Target identification     

Toxicity mechanism of Cu2+ ion individually and in combination with Zn2+ ion in characterizing the molecular changes of Staphylococcus aureus studied using FTIR coupled with chemometric analysis

Copper and zinc have a high binding affinity with a Staphylococcus aureus bacterial community. This causes a change in the biomolecular composition of S. aureus. Our study aims at understanding the resistance mechanism of Cu and Zn either or in various combinations using FTIR and chemometric techniques. Zn toxicity resulted in a significant change in lipid content (3100-2800 cm⁻¹) compared to Cu. A significant decrease in protein content is observed for Cu treatment in the amide region. The bio-concentration factor shows a higher value for Cu compared to Zn. The increase in band area of carbohydrates moieties 1059 cm⁻¹ shows the secretion of EPS due to Cu toxicity. A significant change in nucleic acid compositions was noted in the region1200-900 cm⁻¹ due to Zn treatment. Secondary structural change in protein shows β sheet formation. The result of the finding shows Cu has greater toxicity than Zn. Further toxicity effects were greatly enhanced for metal mixtures ratio (Cu:2Zn). This shows Zn exhibits synergism effect with Cu. The obtained ROC (receiver operating characteristic) curve area gives good reliability of the experiments. The study attempts to understand the mechanism of toxicity removal of Cu and Zn metal mixtures by bacterial population using FTIR coupled with chemometric techniques. Open in a separate windowGraphical abstract     

Mechanisms and innovations: Cardiac stimulation with high voltage discharge from stun guns

The ability of an electrical discharge to stimulate the heart depends on the duration of the pulse, the voltage and the current density that reaches the heart. Stun guns deliver very short electrical pulses with minimal amount of current at high voltages. We discuss external stimulation of the heart by high voltage discharges and review studies that have evaluated the potential of stun guns to stimulate cardiac muscle. Despite theoretical analyses and animal studies which suggest that stun guns cannot and do not affect the heart, 3 independent investigators have shown cardiac stimulation by stun guns. Additional research studies involving people are needed to resolve the conflicting theoretical and experimental findings and to aid in the design of stun guns that are unable to stimulate the heart.Stun guns are used to physically incapacitate a person by discharging controlled electrical energy into the body, thereby preventing effective muscular activity. Although the intention is to provide a safe means of subduing an uncooperative person, some studies have suggested that stun guns can stimulate cardiac muscle in addition to skeletal muscle, thus potentially promoting lethal cardiac arrhythmias. In this article, we review the scientific data about the direct effects of stun gun discharges on the heart during shock delivery. We discuss these issues in terms of electrostimulation and correlate them with theoretical and experimental data in the literature. We discuss the principles of cardiac stimulation from internal and external stimulation and examine the evidence for and against cardiac stimulation by stun gun discharges.