The hippocampus and dopaminergic midbrain: old couple, new insights

Humans have a natural ability to gain new insights by generalizing from previous experience. In this issue of Neuron, Shohamy and Wagner reveal how generalizations naturally emerge during associative learning through a partnership between putatively dopaminergic circuitry in the midbrain and the hippocampus.     

The small protein floodgates are opening; now the functional analysis begins

Aside from a few serendipitous discoveries, small proteins of less than 50 amino acids in bacteria and 100 amino acids in eukaryotes were largely ignored due to challenges in their genetic and biochemical detection. However, with the ever-increasing availability of completed genome sequences and deep sequencing, which allows analysis of genome-wide ribosome occupancy, hundreds of small proteins are now being identified. This brings to the forefront the challenges and opportunities associated with the characterization of these proteins.See research article: http://www.biomedcentral.com/1471-2164/15/946.     

Expansion of Parasite-Specific CD4+ and CD8+ T Cells Expressing IL-10 Superfamily Cytokine Members and Their Regulation in Human Lymphatic Filariasis

Background

Lymphatic filariasis (LF) is known to be associated with an increased production of IL-10. The role of the other IL-10 family members in the pathogenesis of infection and/or disease is not known.

Methodology/Principal Findings

We examined the expression patterns of IL-10 family members – IL-19, IL-24 and IL-26 in LF. We demonstrate that both CD4⁺ and CD8⁺ T cells express IL-19, IL-24 and IL-26 and that the frequency of CD4⁺ T cells expressing IL-19 and IL-24 (as well as IL-10) is significantly increased at baseline and following filarial antigen stimulation in patients with LF in comparison to individuals with filarial lymphedema and uninfected individuals. This CD4⁺ T cell expression pattern was associated with increased production of IL-19 and IL-24 by filarial – antigen stimulated PBMC. Moreover, the frequency of CD4⁺ and CD8⁺ T cells expressing IL-26 was significantly increased following filarial antigen stimulation in filarial lymphedema individuals. Interestingly, IL-10 blockade resulted in diminished frequencies of IL-19⁺ and IL-24⁺ T cells, whereas the addition of recombinant IL-10 resulted in significantly increased frequency of IL-19⁺ and IL-24⁺ T cells as well as significantly up regulated IL-19 and IL-24 gene expression, suggesting that IL-10 regulates IL-19 and IL-24 expression in T cells. In addition, IL-1β and IL-23 blockade also induced a diminution in the frequency of IL-19⁺ and IL-24⁺ T cells, indicating a novel role for these cytokines in the induction of IL-19 and IL-24 expressing T cells. Finally, elimination of infection resulted in significantly decreased frequencies of antigen – specific CD4⁺ T cells expressing IL-10, IL-19 and IL-24.

Conclusions

Our findings, therefore, suggest that IL-19 and IL-24 are associated with the regulation of immune responses in active filarial infection and potentially with protection against development of pathology, while IL-26 is predominantly associated with pathology in LF.     

Parasite-Antigen Driven Expansion of IL-5? and IL-5+ Th2 Human Subpopulations in Lymphatic Filariasis and Their Differential Dependence on IL-10 and TGFβ

Background

Two different Th2 subsets have been defined recently on the basis of IL-5 expression – an IL-5⁺Th2 subset and an IL-5⁻Th2 subset in the setting of allergy. However, the role of these newly described CD4⁺ T cells subpopulations has not been explored in other contexts.

Methods

To study the role of the Th2 subpopulation in a chronic, tissue invasive parasitic infection (lymphatic filariasis), we examined the frequency of IL-5⁺IL-4⁺IL-13⁺ CD4⁺ T cells and IL-5⁻IL-4 IL-13⁺ CD4⁺ T cells in asymptomatic, infected individuals (INF) and compared them to frequencies (F_o) in filarial-uninfected (UN) individuals and to those with filarial lymphedema (CP).

Results

INF individuals exhibited a significant increase in the spontaneously expressed and antigen-induced F_o of both Th2 subpopulations compared to the UN and CP. Interestingly, there was a positive correlation between the F_o of IL-5⁺Th2 cells and the absolute eosinophil and neutrophil counts; in addition there was a positive correlation between the frequency of the CD4⁺IL-5⁻Th2 subpopulation and the levels of parasite antigen – specific IgE and IgG4 in INF individuals. Moreover, blockade of IL-10 and/or TGFβ demonstrated that each of these 2 regulatory cytokines exert opposite effects on the different Th2 subsets. Finally, in those INF individuals cured of infection by anti-filarial therapy, there was a significantly decreased F_o of both Th2 subsets.

Conclusions

Our findings suggest that both IL-5⁺ and IL-5⁻Th2 cells play an important role in the regulation of immune responses in filarial infection and that these two Th2 subpopulations may be regulated by different cytokine-receptor mediated processes.     

Binpairs: Utilization of Illumina Paired-End Information for Improving Efficiency of Taxonomic Binning of Metagenomic Sequences

Motivation

Paired-end sequencing protocols, offered by next generation sequencing (NGS) platforms like Illumia, generate a pair of reads for every DNA fragment in a sample. Although this protocol has been utilized for several metagenomics studies, most taxonomic binning approaches classify each of the reads (forming a pair), independently. The present work explores some simple but effective strategies of utilizing pairing-information of Illumina short reads for improving the accuracy of taxonomic binning of metagenomic datasets. The strategies proposed can be used in conjunction with all genres of existing binning methods.

Results

Validation results suggest that employment of these “Binpairs” strategies can provide significant improvements in the binning outcome. The quality of the taxonomic assignments thus obtained are often comparable to those that can only be achieved with relatively longer reads obtained using other NGS platforms (such as Roche).

Availability

An implementation of the proposed strategies of utilizing pairing information is freely available for academic users at https://metagenomics.atc.tcs.com/binning/binpairs.     

Molecular Markers Reveal Only Two Mud Crab Species of Genus Scylla (Brachyura: Portunidae) in Indian Coastal Waters

The taxonomic ambiguity of the Indian mud crab (genus Scylla de Hann 1833) is still a cause of concern as several papers have been published with misleading identification. This is the first attempt to resolve the taxonomic uncertainty of the mud crab commonly available in Indian coastal waters using molecular genetic markers (ITS-1 and sequencing of COI gene) combined with traditional morphometry. Additionally, we developed a PCR method by which Indian mud crab species can be identified rapidly and effectively. The results clearly indicate that the green morph of the Indian mud crab is Scylla serrata and the brown morph is S. olivacea. The S. serrata commonly mentioned in the literature from India is S. olivacea; the S. tranquebarica noted by many Indian researchers should belong to S. serrata. Caution should be taken when interpreting or implementing the biological, molecular, and aquaculture data in the literature.     

The effect of juvenile hormone and its antagonists on JH esterase activity in Tenebrio molitor

The hemolymph juvenile hormone esterase (JHE) and general carboxyl esterase activities in Tenebrio molitor show independent development-associated changes during larval-pupal and pupal-adult metamorphoses. JHE activity was high in pharate pupae and early pupae. Unlike in lepidopteran pupae that have been studied thus far, JH had no effect on JHE activity in pupae and pharate adults of Tenebrio. A JH antagonist, ethyl 4,2,tert butyl carboxy n benzoate (ETB), and 20-hydroxyecdysone had no effect on JHE activity. These observations suggest that although JHE activity in Tenebrio is precisely regulated during larval-pupal metamorphosis, JH and molting hormone do not appear to be involved in its regulation and that the proximate cues that influence JHE activity in Tenebrio pupae are different from that of lepidopterans.

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Résumé Les activités JHE (estérase juvénile hormone) de l'hémolymphe et carboxyl estérase générale de T. molitor changent indépendamment du développement pendant les métamorphoses larve-nymphe et nymphe-adulte. L'activité JHE est élevée chez les prénymphe et les jeunes nymphes. Contrairement aux chrysalides de papillons, JH n'a pas d'effet sur l'activité JHE chez les nymphes et les préadultes de Tenebrio. Un antagoniste de JH, l'éthyl 4,2,tert butyl carboxy n benzoate (ETB), 20-hydroxyecdysone et le précocène 2-agent anti-allate chez plusieurs insectes-, n'ont aucun effet sur l'activité JHE. Ces observations suggèrent que, bien que l'activité JHE chez T. molitor soit ajustée avec précision pendant la métamorphose larvo-nymphale, JH et hormone de mue ne paraissent pas être impliquées dans sa régulation et que les signaux immédiats, qui influent sur l'activité JHE de la nymphe de T. molitor, diffèrent de ceux des Lépidoptères.

     

Isolation of Natural Naphthoquinones from <Emphasis Type="Italic">Juglans regia</Emphasis> and In Vitro Antioxidant and Cytotoxic Studies of Naphthoquinones and the Synthetic Naphthofuran Derivatives

The naphthoquinones and their derivatives containing hydroxyl group exhibit wide range of pharmacological activities, such as antioxidant, antibacterial, antiviral, anticancer, antimalarial, and antifungal activities. In particular, the antioxidant and anticancer behaviors of these compounds continue to draw attention of researchers. In the present communication, three natural naphthoquinones—juglone, lawsone, and plumbagin—isolated from the chloroform extract of nutshells of Juglans regia Linn. and two 1,4-naphthoquinone derivatives—ethyl-5-hydroxynaphtho[ 1,2-b]furan-3-carboxylate and diethylnaphtho[1,2-b:4,3-b′]difuran-3,4-dicarboxylate—and three 5-hydroxy- 1,4-naphthoquinone derivatives—diethyl-7-hydroxynaphtho[1,2-b:4,3-b']difuran-3,4-dicarboxylate,4-ethoxycarbonyl- 7-hydroxynaphtho[1,2-b:4,3-b']difuran-3-carboxylic acid, and 7-hydroxynaphtho[1,2-b:4,3-b']difuran-3,4- dicarboxylic acid were synthesized and examined for their in vitro antioxidant activity using 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2'-azino-bis-3-ethylbenzthiazoline-6-sulphonic acid (ABTS) bioassays. In addition, the cytotoxicity test using human hepatocellular liver carcinoma cell line (HepG2) was carried out for all the compounds. The 5-hydroxy-1,4-naphthoquinone derivatives displayed almost equivalent scavenging activity in DPPH assay and higher activity in ABTS assay relative to ascorbic acid. On the other hand, naphthoquinones Juglone and Plumbagin showed lesser antioxidant activity, but higher cytotoxic activity than naphthofurans except for diethyl naphtho[1,2-b:4,3-b′]difuran-3,4-dicarboxylate, which showed excellent cytotoxic activity.     

Crystal structure of recombinant triosephosphate isomerase from Bacillus stearothermophilus. An analysis of potential thermostability factors in six isomerases with known three-dimensional structures points to the importance of hydrophobic interactions.

The structure of the thermostable triosephosphate isomerase (TIM) from Bacillus stearothermophilus complexed with the competitive inhibitor 2-phosphoglycolate was determined by X-ray crystallography to a resolution of 2.8 A. The structure was solved by molecular replacement using XPLOR. Twofold averaging and solvent flattening was applied to improve the quality of the map. Active sites in both the subunits are occupied by the inhibitor and the flexible loop adopts the "closed" conformation in either subunit. The crystallographic R-factor is 17.6% with good geometry. The two subunits have an RMS deviation of 0.29 A for 248 C alpha atoms and have average temperature factors of 18.9 and 15.9 A2, respectively. In both subunits, the active site Lys 10 adopts an unusual phi, psi combination. A comparison between the six known thermophilic and mesophilic TIM structures was conducted in order to understand the higher stability of B. stearothermophilus TIM. Although the ratio Arg/(Arg+Lys) is higher in B. stearothermophilus TIM, the structure comparisons do not directly correlate this higher ratio to the better stability of the B. stearothermophilus enzyme. A higher number of prolines contributes to the higher stability of B. stearothermophilus TIM. Analysis of the known TIM sequences points out that the replacement of a structurally crucial asparagine by a histidine at the interface of monomers, thus avoiding the risk of deamidation and thereby introducing a negative charge at the interface, may be one of the factors for adaptability at higher temperatures in the TIM family. Analysis of buried cavities and the areas lining these cavities also contributes to the greater thermal stability of the B. stearothermophilus enzyme. However, the most outstanding result of the structure comparisons appears to point to the hydrophobic stabilization of dimer formation by burying the largest amount of hydrophobic surface area in B. stearothermophilus TIM compared to all five other known TIM structures.