A Case of Post Kala-Azar Dermal Leishmaniasis in India

Post kala-azar dermal leishmaniasis (PKDL) is a rare disease. This is a solitary case report from Orissa, India. We describe a case of PKDL in a 55-year-old male who presented with multiple nodular lesions over face, trunk, and extremities. The patient had been to an endemic area of kala-azar and had a previous history of leishmaniasis. Fine needle aspiration cytology samples from skin nodules revealed Leishmania amastigotes.     

A unified framework for the restoration of Southeast Asian mangroves—bridging ecology, society and economics

The effect of intensive human intervention, poor socio-economic conditions and little knowledge on mangrove ecology pose enormous challenges for mangrove restoration in Southeast Asia. We present a framework for tropical mangrove restoration. Our proposed restoration framework addresses the ecology, economy and social issues simultaneously by considering the causes of mangrove degradation. We provide a step by step guideline for its restoration. We argue that although, ecological issues are of prime importance, economic and social issues must be considered in the restoration plan in order for it to be successful. Since mangrove ecology is not adequately studied in this region, local ecological knowledge can be used to fill the baseline information gaps. Unwanted human disturbance can be minimized by encouraging community participation. This can be ensured and sustained by facilitating the livelihood of the coastal community. We translated the restoration paradigm into a readily available practical guideline for the executors of the plans. We provide an example of mangrove restoration project that is closely related to our proposed framework. We are optimistic that this framework has the potential for universal application with necessary adjustments.     

Identification of gene signatures from RNA-seq data using Pareto-optimal cluster algorithm

Background

Gene signatures are important to represent the molecular changes in the disease genomes or the cells in specific conditions, and have been often used to separate samples into different groups for better research or clinical treatment. While many methods and applications have been available in literature, there still lack powerful ones that can take account of the complex data and detect the most informative signatures.

Methods

In this article, we present a new framework for identifying gene signatures using Pareto-optimal cluster size identification for RNA-seq data. We first performed pre-filtering steps and normalization, then utilized the empirical Bayes test in Limma package to identify the differentially expressed genes (DEGs). Next, we used a multi-objective optimization technique, “Multi-objective optimization for collecting cluster alternatives” (MOCCA in R package) on these DEGs to find Pareto-optimal cluster size, and then applied k-means clustering to the RNA-seq data based on the optimal cluster size. The best cluster was obtained through computing the average Spearman’s Correlation Score among all the genes in pair-wise manner belonging to the module. The best cluster is treated as the signature for the respective disease or cellular condition.

Results

We applied our framework to a cervical cancer RNA-seq dataset, which included 253 squamous cell carcinoma (SCC) samples and 22 adenocarcinoma (ADENO) samples. We identified a total of 582 DEGs by Limma analysis of SCC versus ADENO samples. Among them, 260 are up-regulated genes and 322 are down-regulated genes. Using MOCCA, we obtained seven Pareto-optimal clusters. The best cluster has a total of 35 DEGs consisting of all-upregulated genes. For validation, we ran PAMR (prediction analysis for microarrays) classifier on the selected best cluster, and assessed the classification performance. Our evaluation, measured by sensitivity, specificity, precision, and accuracy, showed high confidence.

Conclusions

Our framework identified a multi-objective based cluster that is treated as a signature that can classify the disease and control group of samples with higher classification performance (accuracy 0.935) for the corresponding disease. Our method is useful to find signature for any RNA-seq or microarray data.

     

Inhibition of a Mitotic Motor Compromises the Formation of Dendrite-like Processes from Neuroblastoma Cells

Microtubules in the axon are uniformly oriented, while microtubules in the dendrite are nonuniformly oriented. We have proposed that these distinct microtubule polarity patterns may arise from a redistribution of molecular motor proteins previously used for mitosis of the developing neuroblast. To address this issue, we performed studies on neuroblastoma cells that undergo mitosis but also generate short processes during interphase. Some of these processes are similar to axons with regard to their morphology and microtubule polarity pattern, while others are similar to dendrites. Treatment with cAMP or retinoic acid inhibits cell division, with the former promoting the development of the axon-like processes and the latter promoting the development of the dendrite-like processes. During mitosis, the kinesin-related motor termed CHO1/MKLP1 is localized within the spindle midzone where it is thought to transport microtubules of opposite orientation relative to one another. During process formation, CHO1/ MKLP1 becomes concentrated within the dendrite-like processes but is excluded from the axon-like processes. The levels of CHO1/MKLP1 increase in the presence of retinoic acid but decrease in the presence of cAMP, consistent with a role for the protein in dendritic differentiation. Moreover, treatment of the cultures with antisense oligonucleotides to CHO1/MKLP1 compromises the formation of the dendrite-like processes. We speculate that a redistribution of CHO1/MKLP1 is required for the formation of dendrite-like processes, presumably by establishing their characteristic nonuniform microtubule polarity pattern.     

Stimulation ofBradyrhizobium japonicum by allelochemicals from green plants

Yeast extract-mannitol broth supplemented with 3 mg.ml⁻¹ extract from aerial parts of plants was noculated withB. japonicum 3I1b110. Filter-sterilized water extracts of foxtail (Setaria viridis), lambsquarters (Chenopodium album), Johnsongrass (Sorghum halepense) and Pennsylvania smartweed (Polygonum pensylvanicum) stimulated growth of the bacterium by 3–4 times after 48 h incubation; however, similar extracts from several other plants were marginally stimulatory. Autoclaved water extracts and methanol (75%) extracts were less stimulatory than filter-sterilized water extracts. Autoclaved water extracts of nutsedge (Cyperus esculentus) and ragweed (Ambrosia psilostachya), and methanol extracts of smartweed, peat and ragweed depressed growth of the bacterium. Filter-sterilized water extracts from shoots of foxtail and lambsquarters increased growth of the bacterium linearly up to 6 mg.ml⁻¹. At that level growth in the presence of lambsquarters shoot extract was almost 20 times that of the control. Comparable growth stimulation by this extract was also found in four other strains ofB. japonicum. The water extracts from roots and stems of lambsquarters, and roots, shoots and inflorescences of foxtail at 3 mg.ml⁻¹ stimulated growth of the bacterium by more than 40 times the control.     

Lagerenyl acetate and lagerenol two tetracyclic triterpenoids with the cycloartane skeleton from Lagerstroemia lancasteri

Lagerenyl acetate and lagerenol two new tetracyclic triterpenoids with the cycloartane skeleton together with four other triterpenoids 2α-hydroxy- 3β-E-p-coumaryloxy-urs-12-en-28-oic acid (jacoumaric acid, isolated as its monoacetylmethylcarboxylate derivative), 2α-hydroxyursolic acid (isolated as its diacetate), germanicyl acetate and friedelin, and sitosterol were isolated from the leaves and twigs of Lagerstroemia lancasteri. The structures of lagerenyl acetate and lagerenol were established as 3β-acetoxycycloart-24-one and 3β-hydroxycycloart-24-one, respectively, on the basis of spectral and chemical evidence.     

Supramolecular conjugates of carbon nanotubes and DNA by a solid-state reaction

DNA-wrapped nanotubes of both multiwalled and single-walled carbon nanotubes were obtained by a solid-state mechanochemical reaction. Scanning electron microscopic images show that the nanotubes were cut into shorter lengths and were fully covered with DNA, which was further confirmed by fluorescence microscopy. This resulted in a high aqueous solubility of the products with a stability of >6 months. The results show that nanotubes were cut also with uniform distribution where >90% of the multiwalled products were 500 nm to 3 microm and 80% of the single-walled products were 250 nm to 1 microm in length, respectively. UV-vis spectra and gel electrophorosis show that the DNA in the product is intact. This facile technique for obtaining supramolecularly masked, water-soluble carbon nanotubes by a solid-state reaction has a great potential for both biological and nonbiological applications of nanotubes.     

Molecular characterization of beta-lactamase genes blaA and blaB of Yersinia enterocolitica biovar 1A

The beta-lactamase genes blaA and blaB were detected by PCR amplification in strains of Yersinia enterocolitica biovar 1A isolated from India, Germany, France and the USA. Both genes were detected in all strains. Polymerase chain reaction-restriction fragment length polymorphism revealed genetic heterogeneity in blaA but not in blaB. Cluster analysis of blaA restriction profiles grouped the strains into three groups. The blaA gene of Y. enterocolitica biovar 1A showed a high degree of sequence homology to that of Y. enterocolitica 8081 (biovar 1B) and Y. enterocolitica Y-56 (biovar 4), whereas homology was low with class A beta-lactamase genes of other members of the family Enterobacteriaceae. The pI 8.7 of enzyme Bla-A of Y. enterocolitica biovar 1A was similar to that of biovars 2, 3 and 4. The enzyme Bla-B focused at 6.8 and 7.1, indicating that biovar 1A strains produced a 'B-like' enzyme. This is the first study to have investigated the genetic heterogeneity of the beta-lactamase genes of Y. enterocolitica.     

Occurrence of Macrosiphum hellebori Theobald & Walton (Hemiptera: Aphididae) in Australia

The European aphid species, Macrosiphum hellebori , the hellebore aphid, is recorded from Australia, having been found in Melbourne, Victoria and in Canberra, Australian Capital Territory, colonising ornamental hellebores, Helleborus species (Ranunculaceae). Insect associates of M. hellebori are recorded, including the hymenopterous primary parasite Lysiphlebus testaceipes (Cresson) (Braconidae: Aphidiinae). Keys are provided for the identification of the three species of Macrosiphum Passerini known from Australia.     

Does post-fire abiotic habitat filtering create divergent plant communities in black spruce forests of eastern Canada?

We investigated the role of post-fire residual organic matter (ROM) thickness as a driver of community assembly in eastern Newfoundland. We hypothesized that if post-fire community assembly is predominantly controlled by ROM thickness (an abiotic habitat filter), then post-fire species composition and functional traits should correspond to the depth and distribution of ROM. However, if species interactions (biotic filter) are the primary constraints on community assembly, then post-fire species composition and their functional traits should be independent of the depth and distribution of ROM. We tested these predictions in three relatively mature plant communities, Kalmia angustifolia heath, black spruce (Picea mariana)-Kalmia shrub savannah and black spruce forest. Through pre-fire stand reconstruction, we found evidence that the three communities originated from black spruce forest. ROM thickness in heath was almost twice that of shrub savannah and six times more than forest, suggesting a gradient in fire severity. Distribution of ROM corresponded to patterns in vegetation dominance, where thick ROM (>2 cm) filtered out black spruce in favour of Kalmia. ROM thickness was a strong predictor of vegetation composition and function between heath and forest, but this was not found between the shrub savannah and forest. We attribute this to species interactions and allelopathy, which may have become important when ROM thickness was suitable for both seed (black spruce) and vegetative (Kalmia) regenerating species. Thus, priority effects or “who came first” may have lead to shrub savannah formation when ROM thickness was ~2 cm. We conclude that abiotic habitat filtering of thick ROM (>2 cm) on (primarily) species’ regeneration traits was the primary driver of community divergence from forest to heath and shrub savannah.