Molecular identification and genetic diversity analysis of sugarcane clones by SSR markers

Sugarcane is one of the important crops with high heterozygosity and phenotypic polymorphism. Varietal identification and characterization is one of the important aspects in any breeding programme. Forty sugarcane clones from Pre -zonal varietal trial (PZVT) conducted at Ugar, North Karnataka were characterized through Simple sequence repeats (SSR) markers using a set of 15 sugarcane specific primer pairs which amplified a total of 164 alleles with an average of 10.93 alleles per pair. Primer NKS 33 was highly polymorphic and produced more than 15 polymorphic alleles and was unique in all the clones studied. Six primers i.e., NKS 2, NKS 6, NKS 7, NKS 40, NKS 42 and NKS 11 were moderately polymorphic by producing 10 to 13 alleles. Percentage of polymorphic bands ranged from 75.0 % (NKS 3) to 100.0 % (NKS 40 and NKS 42). Primers viz., SMC 1039 GC, mSSCIR 54, NKS 2, NKS 7, NKS 9, NKS 33, NKS 40, NKS 42 and NKS 11 were highly informative and generated above 85.0 % of polymorphic bands. Among the primers used, SMC 1039 GC, NKS 33, NKS 42 and NKS 43 produced the maximum number of unique markers in different clones and hence the combined application of these primers will be useful in unambiguous varietal identification. The cluster analysis based on the genetic similarity matrix grouped the 40 clones into two major clusters CI and CII. The largest cluster CII contained the maximum of 38 clones. Cluster C II was further sub-grouped into IIa, IIb, IIc and IId and each sub-cluster comprised 7, 11, 6 and 14 clones respectively. The unique DNA markers and the genetically diverse combinations identified in the present study will enhance the exploitation of genetic diversity present in the clones in breeding programmes and promising twenty eight entries for yield and quality

Unusual Intron Conservation near Tissue-Regulated Exons Found by Splicing Microarrays

Alternative splicing contributes to both gene regulation and protein diversity. To discover broad relationships between regulation of alternative splicing and sequence conservation, we applied a systems approach, using oligonucleotide microarrays designed to capture splicing information across the mouse genome. In a set of 22 adult tissues, we observe differential expression of RNA containing at least two alternative splice junctions for about 40% of the 6,216 alternative events we could detect. Statistical comparisons identify 171 cassette exons whose inclusion or skipping is different in brain relative to other tissues and another 28 exons whose splicing is different in muscle. A subset of these exons is associated with unusual blocks of intron sequence whose conservation in vertebrates rivals that of protein-coding exons. By focusing on sets of exons with similar regulatory patterns, we have identified new sequence motifs implicated in brain and muscle splicing regulation. Of note is a motif that is strikingly similar to the branchpoint consensus but is located downstream of the 5′ splice site of exons included in muscle. Analysis of three paralogous membrane-associated guanylate kinase genes reveals that each contains a paralogous tissue-regulated exon with a similar tissue inclusion pattern. While the intron sequences flanking these exons remain highly conserved among mammalian orthologs, the paralogous flanking intron sequences have diverged considerably, suggesting unusually complex evolution of the regulation of alternative splicing in multigene families

Feature-Weighting-Based Prediction of Drought Occurrence via Two-Stage Particle Swarm Optimization

Drought directly affects environmental sustainability. Predicting the drought at the earliest opportunity will help to execute drought mitigation plans. Several drought indices are used to predict the severity of drought across different geographical regions. The two main drought indices used in India for meteorological drought are the standardized precipitation index (SPI) and standardized precipitation evapotranspiration index (SPEI). This work is a study to find the ability of above mentioned indices to predict meteorological drought for the state of Tamil Nadu using 62 years of data. The prediction results are evaluated using the performance metrics of precision, recall, f1 score, Matthews correlation coefficient, and accuracy. The dataset is severely imbalanced due to the low number of drought incidence years. Hence there exists a tug of war between precision and recall, so for improving it without affecting one another, a multi-objective optimization process is applied. The prediction performance is improved by using the filter-global-supervised feature weighting and wrapper-global-supervised feature weighting techniques. In the filter-based feature weighting approach, the information gain measure and Pearson correlation coefficient are used as feature weights. For the wrapper-based feature weighting approach, two-stage particle swarm optimization (PSO) is designed to calculate the weights of the features, and the random forest is used as the classifier. This two-stage PSO constructs the best population set for individual objectives and then searches around it to find the best particle so that the multiple contradicting objectives will converge into the best solution easier. When compared to classification without feature weighting, two-stage PSO feature weighting achieves a 45% improvement in precision. However, only a moderate improvement in recall is obtained. According to the findings, SPI3 and SPEI12 should be given more weightage in metrological drought prediction

The rho GTPase Rac1 is required for proliferation and survival of progenitors in the developing forebrain

Progenitor cells in the ventricular zone (VZ) and subventricular zone (SVZ) of the developing forebrain give rise to neurons and glial cells, and are characterized by distinct morphologies and proliferative behaviors. The mechanisms that distinguish VZ and SVZ progenitors are not well understood, although the homeodomain transcription factor Cux2 and Cyclin D2, a core component of the cell cycle machinery, are specifically involved in controlling SVZ cell proliferation. Rho GTPases have been implicated in regulating the proliferation, differentiation and migration of many cell types, and one family member, Cdc42, affects the polarity and proliferation of radial glial cells in the VZ. Here we show that another family member, Rac1, is required for the normal proliferation and differentiation of SVZ progenitors and for survival of both VZ and SVZ progenitors. A forebrain-specific loss of Rac1 leads to an SVZ-specific reduction in proliferation, a concomitant increase in cell cycle exit, and premature differentiation. In Rac1 mutants the SVZ and VZ can no longer be delineated, but rather fuse to become a single compact zone of intermingled cells. Cyclin D2 expression, which is normally expressed by both VZ and SVZ progenitors, is reduced in Rac1 mutants, suggesting that the mutant cells differentiate precociously. Rac1-deficient mice can still generate SVZ-derived upper layer neurons, indicating that Rac1 is not required for the acquisition of upper layer neuronal fates, but instead is needed for the normal regulation of proliferation by progenitor cells in the SVZ

Endocytosis regulates cell soma translocation and the distribution of adhesion proteins in migrating neurons

Newborn neurons migrate from their birthplace to their final location to form a properly functioning nervous system. During these movements, young neurons must attach and subsequently detach from their substrate to facilitate migration, but little is known about the mechanisms cells use to release their attachments. We show that the machinery for clathrinmediated endocytosis is positioned to regulate the distribution of adhesion proteins in a subcellular region just proximal to the neuronal cell body. Inhibiting clathrin or dynamin function impedes the movement of migrating neurons both in vitro and in vivo. Inhibiting dynamin function in vitro shifts the distribution of adhesion proteins to the rear of the cell. These results suggest that endocytosis may play a critical role in regulating substrate detachment to enable cell bod

Developmental Transcriptome Analysis of Red-Spotted Apollo Butterfly, Parnassius bremeri

Parnassius bremeri (P. bremeri), a member of the genus Snow Apollo in the swallowtail family (Papilionidae), is a high alpine butterfly that lives in Russia, Korea, and China. It is an endangered wildlife (Class I) in South Korea and is a globally endangered species. The lack of transcriptomic and genomic resources of P. bremeri significantly hinders the study of its population genetics and conservation. The detailed information of the developmental stage-specific gene expression patterns of P. bremeri is of great demand for its conservation. However, the molecular mechanism underlying the metamorphic development of P. bremeri is still unknown. In the present study, the differentially expressed genes (DEGs) across the metamorphic developmental stages were compared using high-throughput transcriptome sequencing. We identified a total of 72,161 DEGs from eight comparisons. GO enrichment analysis showed that a range of DEGs were responsible for cuticle development and the melanin biosynthetic pathway during larval development. Pathway analysis suggested that the signaling pathways, such as the Wnt signaling pathway, hedgehog signaling pathway and Notch signaling pathway, are regulated during the developmental stages of P. bremeri. Furthermore, sensory receptors were also activated, especially during the larval to adult transition stage. Collectively, the results of this study provide a preliminary foundation and understanding of the molecular mechanism in their transcriptomes for further research on the metamorphic development of P. bremeri

Trends in antibiotic resistance in bacterial keratitis isolates from South India

AimsTo report trends in antibiotic resistance in cases of bacterial keratitis from a large eye hospital in South India.MethodsIn this retrospective cross-sectional study, the microbiology laboratory records of patients with infectious keratitis diagnosed at an eye hospital in South India from 2002 to 2013 were reviewed to determine the proportion with antibiotic non-susceptibility.Results3685 bacterial isolates had susceptibility testing performed over the 12-year period. The two most common organisms with resistance were Streptococcus pneumoniae (n=1204) and Pseudomonas aeruginosa (n=894). Antibiotic non-susceptibility was generally uncommon for these two organisms and no significant trends were detected over the course of the study. In contrast, Staphylococcus aureus (N=211) isolates demonstrated a significant increase in fluoroquinolone non-susceptibility over the 12-year study period. This coincided with a significant increase in methicillin-resistant S. aureus (MRSA) during the study period, though the increase in fluoroquinolone resistance was likewise seen in methicillin-sensitive S. aureus (MSSA). For example, ofloxacin resistance in MSSA increased from 11.1% in 2002 to 66.7% in 2013 (p=0.002). No trends were apparent for the aminoglycosides, cefazolin or vancomycin, for which in vitro non-susceptibility generally appeared to be low.ConclusionResistance to antibiotics was generally stable for infectious keratitis isolates from a large eye hospital in South India, except for S. aureus, which experienced a significant increase in fluoroquinolone resistance from 2002 to 2013. Fluoroquinolone antibiotics currently have poor in vitro activity against both MRSA and MSSA in South India and are therefore not the ideal therapy for Staphylococcal corneal ulcers

Genome-wide analysis of differential gene expression and splicing in excitatory neurons and interneuron subtypes

Cortical circuit activity is shaped by the parvalbumin (PV) and somatostatin (SST) interneurons that inhibit principal excitatory (EXC) neurons and the vasoactive intestinal peptide (VIP) interneurons that suppress activation of other interneurons. To understand the molecular-genetic basis of functional specialization and identify potential drug targets specific to each neuron subtype, we performed a genome wide assessment of both gene expression and splicing across EXC, PV, SST and VIP neurons from male and female mouse brains. These results reveal numerous examples where neuron subtype-specific gene expression, as well as splice-isoform usage, can explain functional differences between neuron subtypes, including in presynaptic plasticity, postsynaptic receptor function, and synaptic connectivity specification. We provide a searchable web resource for exploring differential mRNA expression and splice form usage between excitatory, PV, SST, and VIP neurons (http://research-pub.gene.com/NeuronSubtypeTranscriptomes). This resource, combining a unique new dataset and novel application of analysis methods to multiple relevant datasets, identifies numerous potential drug targets for manipulating circuit function, reveals neuron subtype-specific roles for disease-linked genes, and is useful for understanding gene expression changes observed in human patient brains

Fluoroquinolone Treatment and Susceptibility of Isolates From Bacterial Keratitis

OBJECTIVE: To analyze the relationship between fluoroquinolone use at presentation and minimum inhibitory concentration in bacterial keratitis. METHODS: The Steroids for Corneal Ulcers Trial was a randomized, double-masked, placebo-controlled trial assessing the effect of adjunctive topical corticosteroid treatment on outcomes in bacterial keratitis. After presentation, all patients were treated with moxifloxacin hydrochloride, 0.5%. We compare antibiotic use at presentation with minimum inhibitory concentration against moxifloxacin for all isolates. Separate analyses accounted for organism species and fluoroquinolone generation. RESULTS: Topical fluoroquinolone use at presentation was reported in 92 of 480 cases (19.2%). Causative organisms in the 480 cases included Streptococcus pneumoniae (247 cases [51.5%]), Pseudomonas aeruginosa (109 cases [22.7%]), and Nocardia species (55 cases [11.5%]). Isolates from patients who reported fluoroquinolone use at presentation had a 2.01-fold–higher minimum inhibitory concentration (95% CI, 1.39-fold to 2.91-fold; P <.001). Fourth-generation fluoroquinolones were associated with a 3.48-fold–higher minimum inhibitory concentration than those isolates that were not exposed to pretreatment at enrollment (95% CI, 1.99-fold to 6.06-fold; P <.001). CONCLUSION: This study provides evidence that prior use of fluoroquinolones is associated with antibiotic resistance