Overlapping Activities of ELAV/Hu Family RNA Binding Proteins Specify the Extended Neuronal 3' UTR Landscape in Drosophila

The tissue-specific deployment of highly extended neural 3' UTR isoforms, generated by alternative polyadenylation (APA), is a broad and conserved feature of metazoan genomes. However, the factors and mechanisms that control neural APA isoforms are not well understood. Here, we show that three ELAV/Hu RNA binding proteins (Elav, Rbp9, and Fne) have similar capacities to induce a lengthened 3' UTR landscape in an ectopic setting. These factors promote accumulation of chromatin-associated, 3' UTR-extended, nascent transcripts, through inhibition of proximal polyadenylation site (PAS) usage. Notably, Elav represses an unannotated splice isoform of fne, switching the normally cytoplasmic Fne toward the nucleus in elav mutants. We use genomic profiling to reveal strong and broad loss of neural APA in elav/fne double mutant CNS, the first genetic background to largely abrogate this distinct APA signature. Overall, we demonstrate how regulatory interplay and functionally overlapping activities of neural ELAV/Hu RBPs drives the neural APA landscape.

Interplay between positive magnetoresistance and thermoelectric properties by tuning carrier concentration in Sb2-xSnxTe3(x⩽ 0.05) crystals

We report transport properties of Sb2-xSnxTe3(x⩽ 0.05) single crystals, where the tuning of the charge carrier densities via Sn doping significantly improves the magnetoresistance (MR) and the thermoelectric (TE) properties. The MR increases significantly at 2 K forx= 0.01, which reduces considerably with further Sn doping atx= 0.05. The MR results below 90 K forx= 0.01 satisfy the semi-classical two-band approach of Kohler's rule, which does not satisfy the MR results forx= 0.05. At 300 K, the Seebeck coefficient (S) is positive and small forx= 0.01 and it changes the sign with the further increase in Sn doping atx= 0.05 at 300 K. The value of |S| is considerable with an enhancement of the thermoelectric power factor compared to the value forx= 0.01 at 300 K. Analysis of the Hall conductivity indicates the interplay between carrier mobilities and densities, leading to the tuning of MR and TE properties with Sn doping. These results demonstrate that the p-type Sb2Te3becomes n-type with a suitable doping engineering.

Deletion 20q12 is associated with histological transformation of nodal marginal zone lymphoma to diffuse large B-cell lymphoma

The genetic and molecular abnormalities underlying histological transformation (HT) of nodal marginal zone lymphoma (NMZL) to diffuse large B-cell lymphoma (DLBCL) are not well known. While del(20q12) is commonly deleted in myelodysplastic syndrome it has not previously been associated with DLBCL. We recently described a case of DLBCL harboring del(20q12) in a patient with a history of MZL involving lymph nodes and skin. Here we report eight matched cases of transformed MZL(tMZL): six from nodal MZL (tNMZL) and two from splenic MZL (tSMZL). We found >20% del(20q12) in 4/6 tNMZL, but not in tSMZL, nor in unmatched DLBCL, MZL with increased large cells (MZL-ILC), or MZL cases. To examine whether transformation is associated with a specific gene signature, the matched cases were analyzed for multiplexed gene expression using the Nanostring PanCancer Pathways panel. The differential gene expression signature revealed enrichment of inflammatory markers, as previously observed in MZL. Also, tMZL and de novo DLBCL were enriched for extracellular matrix proteins such as collagen and fibronectin, vascular development protein PDGFRβ, DNA repair protein RAD51, and oncogenic secrete protein Wnt11. A subset of genes is expressed differentially in del(20q12) tMZL cases vs non-del(20q12) tMZL cases. These results suggest a specific pathway is involved in the histological transformation of NMZL, which could serve as an indicator of aggressive clinical course in this otherwise indolent neoplasm.

Quantitative earthquake-like statistical properties of the flow of soft materials below yield stress

The flow behavior of soft materials below the yield stress can be rich and is not fully understood. Here, we report shear-stress-induced reorganization of three-dimensional solid-like soft materials formed by closely packed nematic domains of surfactant micelles and a repulsive Wigner glass formed by anisotropic clay nano-discs having ionic interactions. The creep response of both the systems below the yield stress results in angular velocity fluctuations of the shearing plate showing large temporal burst-like events that resemble seismic foreshocks-aftershocks data measuring the ground motion during earthquake avalanches. We find that the statistical properties of the quake events inside such a burst map on to the scaling relations for magnitude and frequency distribution of earthquakes, given by Gutenberg-Richter and Omori laws, and follow a power-law distribution of the inter-occurrence waiting time. In situ polarized optical microscopy reveals that during these events the system self-organizes to a much stronger solid-like state.

Involvement of condensin in cellular senescence through gene regulation and compartmental reorganization

Senescence is induced by various stimuli such as oncogene expression and telomere shortening, referred to as oncogene-induced senescence (OIS) and replicative senescence (RS), respectively, and accompanied by global transcriptional alterations and 3D genome reorganization. Here, we demonstrate that the human condensin II complex participates in senescence via gene regulation and reorganization of euchromatic A and heterochromatic B compartments. Both OIS and RS are accompanied by A-to-B and B-to-A compartmental transitions, the latter of which occur more frequently and are undergone by 14% (430 Mb) of the human genome. Mechanistically, condensin is enriched in A compartments and implicated in B-to-A transitions. The full activation of senescence genes (SASP genes and p53 targets) requires condensin; its depletion impairs senescence markers. This study describes that condensin reinforces euchromatic A compartments and promotes B-to-A transitions, both of which are coupled to optimal expression of senescence genes, thereby allowing condensin to contribute to senescent processes.

Cancer-associated mutations in DICER1 RNase IIIa and IIIb domains exert similar effects on miRNA biogenesis

Somatic mutations in the RNase IIIb domain of DICER1 arise in cancer and disrupt the cleavage of 5' pre-miRNA arms. Here, we characterize an unstudied, recurrent, mutation (S1344L) in the DICER1 RNase IIIa domain in tumors from The Cancer Genome Atlas (TCGA) project and MSK-IMPACT profiling. RNase IIIa/b hotspots are absent from most cancers, but are notably enriched in uterine cancers. Systematic analysis of TCGA small RNA datasets show that DICER1 RNase IIIa-S1344L tumors deplete 5p-miRNAs, analogous to RNase IIIb hotspot samples. Structural and evolutionary coupling analyses reveal constrained proximity of RNase IIIa-S1344 to the RNase IIIb catalytic site, rationalizing why mutation of this site phenocopies known hotspot alterations. Finally, examination of DICER1 hotspot endometrial tumors reveals derepression of specific miRNA target signatures. In summary, comprehensive analyses of DICER1 somatic mutations and small RNA data reveal a mechanistic aspect of pre-miRNA processing that manifests in specific cancer settings.

Diagnosing osteoarthritis from T2 maps using deep learning: an analysis of the entire Osteoarthritis Initiative baseline cohort

OBJECTIVE

We aim to study to what extent conventional and deep-learning-based T2 relaxometry patterns are able to distinguish between knees with and without radiographic osteoarthritis (OA).

METHODS

T2 relaxation time maps were analyzed for 4,384 subjects from the baseline Osteoarthritis Initiative (OAI) Dataset. Voxel Based Relaxometry (VBR) was used for automatic quantification and voxel-based analysis of the differences in T2 between subjects with and without radiographic OA. A Densely Connected Convolutional Neural Network (DenseNet) was trained to diagnose OA from T2 data. For comparison, more classical feature extraction techniques and shallow classifiers were used to benchmark the performance of our algorithm's results. Deep and shallow models were evaluated with and without the inclusion of risk factors. Sensitivity and Specificity values and McNemar test were used to compare the performance of the different classifiers.

RESULTS

The best shallow model was obtained when the first ten Principal Components, demographics and pain score were included as features (AUC = 77.77%, Sensitivity = 67.01%, Specificity = 71.79%). In comparison, DenseNet trained on raw T2 data obtained AUC = 83.44%, Sensitivity = 76.99%, Specificity = 77.94%. McNemar test on two misclassified proportions form the shallow and deep model showed that the boost in performance was statistically significant (McNemar's chi-squared = 10.33, degree of freedom (DF) = 1, P-value = 0.0013).

CONCLUSION

In this study, we presented a Magnetic Resonance Imaging (MRI)-based data-driven platform using T2 measurements to characterize radiographic OA. Our results showed that feature learning from T2 maps has potential in uncovering information that can potentially better diagnose OA than simple averages or linear patterns decomposition.

Towards prevention of post-traumatic osteoarthritis: report from an international expert working group on considerations for the design and conduct of interventional studies following acute knee injury

OBJECTIVE

There are few guidelines for clinical trials of interventions for prevention of post-traumatic osteoarthritis (PTOA), reflecting challenges in this area. An international multi-disciplinary expert group including patients was convened to generate points to consider for the design and conduct of interventional studies following acute knee injury.

DESIGN

An evidence review on acute knee injury interventional studies to prevent PTOA was presented to the group, alongside overviews of challenges in this area, including potential targets, biomarkers and imaging. Working groups considered pre-identified key areas: eligibility criteria and outcomes, biomarkers, injury definition and intervention timing including multi-modality interventions. Consensus agreement within the group on points to consider was generated and is reported here after iterative review by all contributors.

RESULTS

The evidence review identified 37 studies. Study duration and outcomes varied widely and 70% examined surgical interventions. Considerations were grouped into three areas: justification of inclusion criteria including the classification of injury and participant age (as people over 35 may have pre-existing OA); careful consideration in the selection and timing of outcomes or biomarkers; definition of the intervention(s)/comparator(s) and the appropriate time-window for intervention (considerations may be particular to intervention type). Areas for further research included demonstrating the utility of patient-reported outcomes, biomarkers and imaging outcomes from ancillary/cohort studies in this area, and development of surrogate clinical trial endpoints that shorten the duration of clinical trials and are acceptable to regulatory agencies.

CONCLUSIONS

These considerations represent the first international consensus on the conduct of interventional studies following acute knee joint trauma.

Metamagnetic transition and observation of spin-fluctuations in the antiferromagnetic Heusler compound Pd2MnIn

We report detailed investigations on the structural, magnetic, magneto-transport and calorimetric aspects of a partially ordered Heusler compound Pd₂MnIn. The sample shows antiferomagnetic (AFM) state below around 120 K, though positive paramagnetic Curie temperature signifies a complex magnetic ground state with the presence of both ferromagnetic (FM) and AFM correlations. A clear spin-flop type metamagnetic transition is observed as evident from the magnetization and resistivity data. However, non-saturation of magnetization even at 145 kOe of applied field implies that the high field state may be a spin canted state, originating from the enhanced FM correlations by field induced conduction electron spin polarization. The sample shows a profound quadratic temperature dependence of resistivity below about 20-25 K indicating a spin-fluctuation dominated low temperature region. Previous electronic structure calculations show the existence of a subtle balance between superexchange mediated AFM state and an RKKY (Ruderman-Kittel-Kasuya-Yoshida) interaction mediated FM state in Pd₂MnIn. Such competing AFM-FM correlations can be accounted for the observed spin fluctuations.

CRISPR RNA-guided DNA cleavage by reconstituted Type I-A immune effector complexes

Diverse CRISPR-Cas immune systems protect archaea and bacteria from viruses and other mobile genetic elements. All CRISPR-Cas systems ultimately function by sequence-specific destruction of invading complementary nucleic acids. However, each CRISPR system uses compositionally distinct crRNP [CRISPR (cr) RNA/Cas protein] immune effector complexes to recognize and destroy invasive nucleic acids by unique molecular mechanisms. Previously, we found that Type I-A (Csa) effector crRNPs from Pyrococcus furiosus function in vivo to eliminate invader DNA. Here, we reconstituted functional Type I-A effector crRNPs in vitro with recombinant Csa proteins and synthetic crRNA and characterized properties of crRNP assembly, target DNA recognition and cleavage. Six proteins (Csa 4-1, Cas3″, Cas3', Cas5a, Csa2, Csa5) are essential for selective target DNA binding and cleavage. Native gel shift analysis and UV-induced RNA-protein crosslinking demonstrate that Cas5a and Csa2 directly interact with crRNA 5' tag and guide sequences, respectively. Mutational analysis revealed that Cas3″ is the effector nuclease of the complex. Together, our results indicate that DNA cleavage by Type I-A crRNPs requires crRNA-guided and protospacer adjacent motif-dependent target DNA binding to unwind double-stranded DNA and expose single strands for progressive ATP-dependent 3'-5' cleavage catalyzed by integral Cas3' helicase and Cas3″ nuclease crRNP components.

DICER1 Is Essential for Self-Renewal of Human Embryonic Stem Cells

MicroRNAs (miRNAs) are the effectors of a conserved gene-silencing system with broad roles in post-transcriptional regulation. Due to functional overlaps, assigning specific functions to individual miRNAs has been challenging. DICER1 cleaves pre-miRNA hairpins into mature miRNAs, and previously Dicer1 knockout mouse embryonic stem cells have been generated to study miRNA function in early mouse development. Here we report an essential requirement of DICER1 for the self-renewal of human embryonic stem cells (hESCs). Utilizing a conditional knockout approach, we found that DICER1 deletion led to increased death receptor-mediated apoptosis and failure of hESC self-renewal. We further devised a targeted miRNA screening strategy and uncovered essential pro-survival roles of members of the mir-302-367 and mir-371-373 clusters that bear the seed sequence AAGUGC. This platform is uniquely suitable for dissecting the roles of individual miRNAs in hESC self-renewal and differentiation, which may help us better understand the early development of human embryos.

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Conditional DICER1 knockouts enable the study of its essential requirement in hESCs

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DICER1 deletion leads to increased extrinsic (receptor-mediated) apoptosis

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miRNAs rescue the DICER1 knockout apoptotic phenotype

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This work provides a platform for interrogating miRNA function in hESCs

Mathematical structural descriptors and mutagenicity assessment: a study with congeneric and diverse datasets$

Quantitative bioactivity and toxicity assessment of chemical compounds plays a central role in drug discovery as it saves a substantial amount of resources. To this end, high-performance computing has enabled researchers and practitioners to leverage hundreds, or even thousands, of computed molecular descriptors for the activity prediction of candidate compounds. In this paper, we evaluate the utility of two large groups of chemical descriptors by such predictive modelling, as well as chemical structure discovery, through empirical analysis. We use a suite of commercially available and in-house software to calculate molecular descriptors for two sets of chemical mutagens - a homogeneous set of 95 amines, and a diverse set of 508 chemicals. Using calculated descriptors, we model the mutagenic activity of these compounds using a number of methods from the statistics and machine-learning literature, and use robust principal component analysis to investigate the low-dimensional subspaces that characterize these chemicals. Our results suggest that combining different sets of descriptors is likely to result in a better predictive model - but that depends on the compounds being modelled and the modelling technique being used.

Coexisting exchange bias effect and ferroelectricity in geometrically frustrated ZnCr2O4

Concomitant occurrence of exchange bias effect and ferroelectric order is revealed in antiferromagnetic spinel ZnCr₂O₄. The exchange bias effect is observed below antiferromagnetic Neél temperature (T _N) with a reasonable value of exchange bias field ([Formula: see text] Oe at 2 K). Intriguingly, the [Formula: see text] ratio is found unusually high as  ∼2.2, where H _C is the coercivity. This indicates that large H _C is not always primary for obtaining large exchange bias effect. Ferroelectric order is observed at T _N, where non-centrosymmetric magnetic structure with [Formula: see text] space group associated with the magnetoelectric coupling correlates the ferroelectric order, proposing that, ZnCr₂O₄ is an improper multiferroic material. Rare occurrence of exchange bias effect and ferroelectric order in ZnCr₂O₄ attracts the community for fundamental interest and draws special attention in designing new materials for possible electric field control of exchange bias effect.

Effect of dietary manipulation and vaccination of turkey breeder hens on immunoglobulin levels of yolk, yolk sac and neonate poults

Two hundred turkey breeder hens and 24 viable toms of 30-35 weeks age of small white variety were distributed into two treatment groups having four replicates of 25 hens and three toms in each treatment. First four replicates were offered a turkey breeder diet (Diet A) (Nutrient requirements of poultry, 1994, National Academic Press, Washington, DC) and the rest four replicates were maintained on a higher plane of nutrition (Diet B) for 8-week duration. After 6 weeks of experimental feeding, two replicates from each treatment groups were vaccinated with ND (R₂ B) vaccine. Yolk sac of embryo from birds fed Diet B had a significantly higher (p < .05) IgG, IgM level and HI titre (log 2) than those fed Diet A. HI titre values of embryonic yolk sac from the vaccinated birds fed Diet B were significantly higher (p < .05) than that of the control groups. In addition, HI titre values were significantly higher (p < .05) in the day-old poults of the birds fed Diet B than that of those fed Diet A. There was significantly (p < .01) positive correlation between serum IgG and IgM of the breeder birds and day-old chicks. Similarly, there was significantly (p < .05) positive correlation between yolk IgG and IgM after 1-month experimental feeding and yolk sac IgG and IgM. Positive correlation (p < .05) also existed between yolk sac IgM and day-old chick serum IgM. Furthermore, the HI titres of breeder birds' serum at 14 days post-vaccination were positively correlated with their egg yolk after 10 and 15 days post-vaccination, yolk sac and day-old chicks. Thus, the study envisaged that a higher immunity in neonate poults from turkey breeders maintained on a higher plane of nutrition may be elicited as there was maternal transfer of antibodies from the serum of breeder birds to their offsprings through their yolk sac.

Glassy magnetic ground state and Kondo-like behaviour in Mn10FeGe8 alloy

We report a detailed investigation of the ground-state magnetic properties of newly synthesized [Formula: see text] [Formula: see text] alloy. The sample can be thought of being derived by substituting one Mn atom by Fe of the parent compound [Formula: see text] [Formula: see text]. Fe-substitution leads to a drastic change in the magnetic ground state as well as to the magneto-transport properties of the parent alloy. On cooling below 250 K, [Formula: see text] [Formula: see text] undergoes a transition from paramagnetic phase to a state having significant ferromagnetic correlations. The ground state is found to be canonical spin glass (CSG) type in nature as evident from the dc magnetization and ac susceptibility measurements. Interestingly, the resistivity data shows an upturn at low temperature below about 30 K, mimicking Kondo-like behaviour. [Formula: see text] [Formula: see text] turns out to be a rare example among 3d transition metal alloys, where a Kondo-like state coexists within a CSG phase.