Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome

Two novel mitochondrial gene arrangements are identified in an agamid lizard and a ranid frog. Statistical tests incorporating phylogeny indicate a link between novel vertebrate mitochondrial gene orders and movement of the origin of light-strand replication. A mechanism involving errors in light-strand replication and tandem duplication of genes is proposed for rearrangement of vertebrate mitochondrial genes. A second mechanism involving small direct repeats also is identified. These mechanisms implicate gene order as a reliable phylogenetic character. Shifts in gene order define major lineages without evidence of parallelism or reversal. The loss of the origin of light-strand replication from its typical vertebrate position evolves in parallel and, therefore, is a less reliable phylogenetic character. Gene junctions also evolve in parallel. Sequencing across multigenic regions, in particular transfer RNA genes, should be a major focus of future systematic studies to locate novel gene orders and to provide a better understanding of the evolution of the vertebrate mitochondrial genome.      

Fabrication of Sub‐Micrometer‐Thick Solid Electrolyte Membranes of β‐Li3PS4 via Tiled Assembly of Nanoscale,Plate‐Like Building Blocks

Solid electrolytes represent a critical component in future batteries that provide higher energy and power densities than the current lithium‐ion batteries. The potential of using ultrathin films is among the best merits of solid electrolytes for considerably reducing the weight and volume of each battery unit, thereby significantly enhancing the energy density. However, it is challenging to fabricate ultrathin membranes of solid electrolytes using the conventional techniques. Here, a new strategy is reported for fabricating sub‐micrometer‐thick membranes of β‐Li₃PS₄ solid electrolytes via tiled assembly of shape‐controlled, nanoscale building blocks. This strategy relies on facile, low‐cost, solution‐based chemistry to create membranes with tunable thicknesses. The ultrathin membranes of β‐Li₃PS₄ show desirable ionic conductivity and necessary compatibility with metallic lithium anodes. The results of this study also highlight a viable strategy for creating ultrathin, dense solid electrolytes with high ionic conductivities for the next‐generation energy storage and conversion systems.     

Reorganization of metastamiRs in the evolution of metastatic aggressive neuroblastoma cells

Background

MetastamiRs have momentous clinical relevance and have been correlated with disease progression in many tumors. In this study, we identified neuroblastoma metastamiRs exploiting unique mouse models of favorable and high-risk metastatic human neuroblastoma. Further, we related their deregulation to the modulation of target proteins and established their association with clinical outcomes.

Results

Whole genome miRNA microarray analysis identified 74 metastamiRs across the manifold of metastatic tumors. RT-qPCR on select miRNAs validated profile expression. Results from bio-informatics across the ingenuity pathway, miRCancer, and literature data-mining endorsed the expression of these miRNAs in multiple tumor systems and showed their role in metastasis, identifying them as metastamiRs. Immunoblotting and TMA-IHC analyses revealed alterations in the expression/phosphorylation of metastamiRs’ targets, including ADAMTS-1, AKT1/2/3, ASK1, AURKβ, Birc1, Birc2, Bric5, β-CATENIN, CASP8, CD54, CDK4, CREB, CTGF, CXCR4, CYCLIN-D1, EGFR, ELK1, ESR1, CFOS, FOSB, FRA, GRB10, GSK3β, IL1α, JUND, kRAS, KRTAP1, MCP1, MEGF10, MMP2, MMP3, MMP9, MMP10, MTA2, MYB, cMYC, NF2, NOS3, P21, pP38, PTPN3, CLEAVED PARP, PKC, SDF-1β, SEMA3D, SELE, STAT3, TLR3, TNFα, TNFR1, and VEGF in aggressive cells ex vivo and in a manifold of metastatic tumors in vivo. miRNA mimic (hsa-miR-125b, hsa-miR-27b, hsa-miR-93, hsa-miR-20a) and inhibitor (hsa-miR-1224-3p, hsa-miR-1260) approach for select miRNAs revealed the direct influence of the altered metastamiRs in the regulation of identified protein targets. Clinical outcome association analysis with the validated metastamiRs’ targets corresponded strongly with poor overall and relapse-free survival.

Conclusions

For the first time, these results identified a comprehensive list of neuroblastoma metastamiRs, related their deregulation to altered expression of protein targets, and established their association with poor clinical outcomes. The identified set of distinctive neuroblastoma metastamiRs could serve as potential candidates for diagnostic markers for the switch from favorable to high-risk metastatic disease.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1642-x) contains supplementary material, which is available to authorized users.     

FDTD Study on Evolution of Trimer Silver@Silica Nanospheres to Dimer for SERS Characteristics

Light enhancement occurs strongly within the plasmonic clusters by interaction with surface plasmons. Surface-enhanced Raman spectroscopic (SERS) characteristics of a series of silver@silica trimer core–shell (CS) nanosphere (NS) clusters are investigated in this paper. It is significant to understand the electric field (EF) enhancement mechanism behind the SERS technique. The effect of symmetry breaking is studied for the series starting from the highly symmetric trimer cluster and transformed to linear dimer geometry which progresses through the gradual reduction in the vertex NS. The optical activity such as the evolution of LSPR peak is discussed, the formation of hot spots is demonstrated and the strength of the local EF enhancement is calculated and correlated with the plasmon dipolar modes by using plasmon hybridization theory to understand the underlying physical concepts.

     

Regulatory role of cathepsin L in induction of nuclear laminopathy in Alzheimer’s disease

Experimental and clinical therapies in the field of Alzheimer''s disease (AD) have focused on elimination of extracellular amyloid beta aggregates or prevention of cytoplasmic neuronal fibrillary tangles formation, yet these approaches have been generally ineffective. Interruption of nuclear lamina integrity, or laminopathy, is a newly identified concept in AD pathophysiology. Unraveling the molecular players in the induction of nuclear lamina damage may lead to identification of new therapies. Here, using 3xTg and APP/PS1 mouse models of AD, and in vitro model of amyloid beta42 (Aβ42) toxicity in primary neuronal cultures and SH‐SY5Y neuroblastoma cells, we have uncovered a key role for cathepsin L in the induction of nuclear lamina damage. The applicability of our findings to AD pathophysiology was validated in brain autopsy samples from patients. We report that upregulation of cathepsin L is an important process in the induction of nuclear lamina damage, shown by lamin B1 cleavage, and is associated with epigenetic modifications in AD pathophysiology. More importantly, pharmacological targeting and genetic knock out of cathepsin L mitigated Aβ42 induced lamin B1 degradation and downstream structural and molecular changes. Affirming these findings, overexpression of cathepsin L alone was sufficient to induce lamin B1 cleavage. The proteolytic activity of cathepsin L on lamin B1 was confirmed using mass spectrometry. Our research identifies cathepsin L as a newly identified lamin B1 protease and mediator of laminopathy observed in AD. These results uncover a new aspect in the pathophysiology of AD that can be pharmacologically prevented, raising hope for potential therapeutic interventions.     

Studies on the utilization of single cell protein by the silkworm Bombyx mori

Final-instar larvae of Bombyx mori fed mulberry leaves, supplemented with Spirulina fusiformis (Woronichin) as a source of single cell protein (SCP), required 6 days to attain a maximum larval weight of 2090 mg; control group larvae needed 9 days to attain a final larval weight of 1470 mg. Quantity of feeding, assimilation and conversion efficiencies increased substantially in the SCP-fed group. Significant improvements in the economic characters such as cocoon, pupal, and shell weights were obtained in the SCP supplemented larvae in comparison to the normal leaf fed larvae. About 15% of the labelled S. fusiformis was directly incorporated into larval tissue. Presence of SCP in the gut facilitated better conversion of consumed leaf protein.

---

Etudes sur l'utilisation des protéines de cellules isolées par le ver à soie, Bombyx mori

Résumé Des chenilles du dernier stade de Bombyx mori, alimentées sur mûrier additionné de Spirulina fusiformis comme source de protéine de cellule isolée (SCP), atteignent en 6 jours le poids larvaire maximum de 2090 mg; les chenilles témoins consommaient pendant 9 jours pour obtenir leur poids larvaire final de 1470 mg. Les quantités consommées, les coefficients d'assimilation et de conversion ont augmenté substantiellement chez les chenilles avec SCP. Des augmentations significatives de critères économiques, comme les poids de cocon, de nymphe et de cogul, ont été observées avec l'addition de SCP par rapport aux témoins. Environ 15% du S. fusiformis marqué a été incorporé directement dans les tissus larvaires. La présence de SCP dans l'intestin a permis une meilleure conversion des protéines foliaires consommées.

     

Studies on predation of the mosquito Culex fatigans by Rana tigrina tadpoles

Satiated predation, predation rate and prey preference of different weight groups of Rana tigrina (Daud) tadpoles on different larval and pupal stages of Culex fatigans were studied. Irrespective of the prey and predator size, the satiation time remained more or less equal. There exists a mass-dependent predation: Calculated predation rates or predatory constants (Kpr) showed that I instar prey was preyed upon at about equal rate, while other instars and pupa showed an increasing trend with increasing body weight of the predator. The prey preference assessed using the Kpr, revealed that prey size is an important parameter in predation. The R. tigrina tadpole is a more efficient pupal predator than other mosquito predators.     

Evolutionary relationships among the male and female mitochondrial DNA lineages in the Mytilus edulis species complex

A novel form of mitochondrial DNA (mtDNA) inheritance has previously been documented for the blue mussel (Mytilus edulis). Female mussels inherit their mtDNA solely from their mother while males inherit mtDNA from both their mother and their father. In males, the paternal mtDNA is preferentially amplified so that the male gonad is highly enriched for the paternal mtDNA that is then transmitted from fathers to sons. We demonstrate that this mode of mtDNA inheritance also operates in the closely related species M. galloprovincialis and M. trossulus. The evolutionary relationship between the male and female mtDNA lineages is estimated by phylogenetic analysis of 455 nucleotides from the large subunit ribosomal RNA gene. We have found that the male and female lineages are highly divergent; the divergence of these lineages began prior to the speciation of the three species of blue mussels. Further, the separation between the male and female lineages is estimated to have occurred between 5.3 and 5.7 MYA.