Anisotropic magnetic and superconducting properties of pure and Co-doped CaFe2_2As2_2 single crystals

We report anisotropic dc magnetic susceptibility $\chi(T)$, electrical resistivity $\rho(T)$, and heat capacity $C(T)$ measurements on the single crystals of CaFe$_{2-x}$Co$_x$As$_2$ for $x$ = 0 and 0.06. Large sized single crystals were grown by the high temperature solution method with Sn as the solvent. For the pure compound with $x$ = 0, a high temperature transition at 170 K is observed which is attributed to a combined spin density wave (SDW) ordering and a structural phase transition. On the other hand, for the Co-doped samples for $x$ = 0.06, the SDW transition is suppressed while superconductivity is observed at $\simeq$17 K. The superconducting transition has been confirmed from the magnetization and electrical resistivity studies. The $^{57}$Fe M\"ossbauer spectrum in CaFe$_2$As$_2$ indicates that the SDW ordering is incommensurate. In the Co-doped sample, a prominent paramagnetic line at 4.2 K is observed indicating a weakening of the SDW state.Comment: 4 pages 5 figures. Submitted to Phys. Rev.

Crystal Growth and Anisotropic Magnetic Properties of RAg2_2Ge2_2 (R = Pr, Nd and Sm) Single Crystals

We report the single crystal growth and anisotropic magnetic properties of the tetragonal RAg$_2$Ge$_2$ (R = Pr, Nd and Sm) compounds which crystallize in the ThCr$_2$Si$_2$ type crystal structure with the space group \textit{I4/mmm}. The single crystals of RAg$_2$Ge$_2$ (R = Pr, Nd and Sm) were grown by self-flux method using Ag:Ge binary alloy as flux. From the magnetic studies on single crystalline samples we have found that PrAg$_2$Ge$_2$ and NdAg$_2$Ge$_2$ order antiferromagnetically at 12 K and 2 K respectively, thus corroborating the earlier polycrystalline results. SmAg$_2$Ge$_2$ also orders antiferromagnetically at 9.2 K. The magnetic susceptibility and magnetization show a large anisotropy and the easy axis of magnetization for PrAg$_2$Ge$_2$ and NdAg$_2$Ge$_2$ is along the [100] direction where as it changes to [001] direction for SmAg$_2$Ge$_2$. Two metamagnetic transitions were observed in NdAg$_2$Ge$_2$ at $H_{\rm m1}$ = 1.25 T and $H_{\rm m2}$ =3.56 T for the field parallel to [100] direction where as the magnetization along [001] direction was linear indicating the hard axis of magnetization.Comment: 4 pages, 4 figures, submitted to SCES-2008 Proceedings. Submitted to SCES - 2008 Proceeding

Crystal structure of 2-benzylamino-4-(4-bromo-phenyl)-6,7-dihydro-5H-cyclopenta[b]pyridine-3-carbonitrile

JS and RAN thank the management of The Madura College (Autonomous), Madurai, for their encouragement and support. RRK thanks the University Grants Commission, New Delhi, for funds through Major Research Project F. No. 42–242/2013 (SR).Peer reviewedPublisher PD

IL-22 mediates goblet cell hyperplasia and worm expulsion in intestinal helminth infection.

Type 2 immune responses are essential in protection against intestinal helminth infections. In this study we show that IL-22, a cytokine important in defence against bacterial infections in the intestinal tract, is also a critical mediator of anti-helminth immunity. After infection with Nippostrongylus brasiliensis, a rodent hookworm, IL-22-deficient mice showed impaired worm expulsion despite normal levels of type 2 cytokine production. The impaired worm expulsion correlated with reduced goblet cell hyperplasia and reduced expression of goblet cell markers. We further confirmed our findings in a second nematode model, the murine whipworm Trichuris muris. T.muris infected IL-22-deficient mice had a similar phenotype to that seen in N.brasiliensis infection, with impaired worm expulsion and reduced goblet cell hyperplasia. Ex vivo and in vitro analysis demonstrated that IL-22 is able to directly induce the expression of several goblet cell markers, including mucins. Taken together, our findings reveal that IL-22 plays an important role in goblet cell activation, and thus, a key role in anti-helminth immunity

CNV-seq, a new method to detect copy number variation using high-throughput sequencing

<p>Abstract</p> <p>Background</p> <p>DNA copy number variation (CNV) has been recognized as an important source of genetic variation. Array comparative genomic hybridization (aCGH) is commonly used for CNV detection, but the microarray platform has a number of inherent limitations.</p> <p>Results</p> <p>Here, we describe a method to detect copy number variation using shotgun sequencing, CNV-seq. The method is based on a robust statistical model that describes the complete analysis procedure and allows the computation of essential confidence values for detection of CNV. Our results show that the number of reads, not the length of the reads is the key factor determining the resolution of detection. This favors the next-generation sequencing methods that rapidly produce large amount of short reads.</p> <p>Conclusion</p> <p>Simulation of various sequencing methods with coverage between 0.1× to 8× show overall specificity between 91.7 – 99.9%, and sensitivity between 72.2 – 96.5%. We also show the results for assessment of CNV between two individual human genomes.</p

A Powerful Method for Transcriptional Profiling of Specific Cell Types in Eukaryotes: Laser-Assisted Microdissection and RNA Sequencing

The acquisition of distinct cell fates is central to the development of multicellular organisms and is largely mediated by gene expression patterns specific to individual cells and tissues. A spatially and temporally resolved analysis of gene expression facilitates the elucidation of transcriptional networks linked to cellular identity and function. We present an approach that allows cell type-specific transcriptional profiling of distinct target cells, which are rare and difficult to access, with unprecedented sensitivity and resolution. We combined laser-assisted microdissection (LAM), linear amplification starting from <1 ng of total RNA, and RNA-sequencing (RNA-Seq). As a model we used the central cell of the Arabidopsis thaliana female gametophyte, one of the female gametes harbored in the reproductive organs of the flower. We estimated the number of expressed genes to be more than twice the number reported previously in a study using LAM and ATH1 microarrays, and identified several classes of genes that were systematically underrepresented in the transcriptome measured with the ATH1 microarray. Among them are many genes that are likely to be important for developmental processes and specific cellular functions. In addition, we identified several intergenic regions, which are likely to be transcribed, and describe a considerable fraction of reads mapping to introns and regions flanking annotated loci, which may represent alternative transcript isoforms. Finally, we performed a de novo assembly of the transcriptome and show that the method is suitable for studying individual cell types of organisms lacking reference sequence information, demonstrating that this approach can be applied to most eukaryotic organisms