Genome sequencing and assembly of Indian golden silkmoth, Antheraea assamensis Helfer (Saturniidae, Lepidoptera).

Muga silkworm (Antheraea assamensis), one of the economically important wild silkmoths, is unique among saturniid silkmoths. It is confined to the North-eastern part of India. Muga silk has the highest value among the other silks. Unlike other silkmoths, A. assamensis has a low chromosome number (n = 15), and ZZ/ZO sex chromosome system. Here, we report the first high-quality draft genome of A. assamensis, assembled by employing the Illumina and PacBio sequencing platforms. The assembled genome of A. assamensis is 501.18 Mb long, with 2697 scaffolds and an N50 of 683.23 Kb. The genome encompasses 18,385 protein-coding genes, 86.29% of which were functionally annotated. Phylogenetic analysis of A. assamensis revealed its divergence from other Antheraea species approximately 28.7 million years ago. Moreover, an investigation into detoxification-related gene families, CYP450, GST, and ABC-transporter, revealed a significant expansion in A. assamensis as compared to the Bombyx mori. This expansion is comparable to Spodoptera litura, suggesting adaptive responses linked to the polyphagous behavior observed in these insects. This study provides valuable insights into the molecular basis of evolutionary divergence and adaptations in muga silkmoth. The genome assembly reported in this study will significantly help in the functional genomics studies on A. assamensis and other Antheraea species along with comparative genomics analyses of Bombycoidea insects.

Molecular characterization of non-biogenic amines producing Lactobacillus plantarum GP11 isolated from traditional pickles using HRESI-MS analysis.

Fungal spoilage and toxic biogenic amine production is a major risk in fermented products. Therefore, the selection of nontoxic biogenic amines producing probiotic bacteria plays a vital role in the fermentation process. In the present study, a total of 18 bacterial isolates were isolated from eight different homemade pickle samples and 15 lactic acid bacteria (LAB) were identified based on biochemical tests. Out of which only seven isolates (GP1, GP2, GP3, GP4, GP5, GP9, and GP11) exhibited antifungal activity against pickle contaminant Aspergillus sp and Penicillium sp. Among the potential LAB isolates, GP11 showed the highest antifungal activity against Aspergillus sp and Penicillium sp with a zone of inhibition 28.33 ± 0.57and 19.66 ± 0.57 mm respectively. The potent LAB isolates were tested for amino acid decarboxylase activity, in which GP2, GP3, GP4, and GP5 exhibited to produce tyramine, cadaverine, and phenylethylamine while GP1 and GP5 have produced tyramine and phenylethylamine respectively. However, highly potent antifungal active isolate GP11 did not produce biogenic amine. Further, GP1, GP9, and GP11 were subjected to confirmation of biogenic amines production using HRESI-MS. HRESI-MS analysis of the GP1 and GP9 sample confirmed the presence of phenylethylamine and tyramine respectively. Interestingly, GP11 isolate did not show any biogenic amines production and GP11 was further subjected to 16S rRNA typing and identified as Lactobacillus plantarum. On in situ pickle sensory evaluation, GP11 lactopickle was graded as very good quality when compared to traditional one. Therefore L. plantarum GP11 could be developed as an ideal starter culture for the fermented production of a pickle.

Genome wide characterization revealed MnMLO2 and MnMLO6A as candidate genes involved in powdery mildew susceptibility in mulberry.

Mulberry is a fast growing economically important tree for sericulture industry and contains compounds for preventing and treating several diseases and ailments. The quality and quantity of mulberry leaf available to produce silk fibre and for medicinal purpose is greatly affected by number of foliar diseases, out of which powdery mildew is the major one. Imparting genetic resistance becomes an important approach in disease management in mulberry as spraying of fungicides has harmful effects on silkworm growth and development. Deployment of non-functional susceptible genes such as Mildew resistance Locus O (MLO) against powdery mildew in few crops stimulated to identify and characterize MLO genes in mulberry. In this study, genome wide analysis identified 16 MLO genes in Morus notabilis. Phylogenetic analysis found that MnMLO2, MnMLO6A, MnMLO6B, MnMLO12A and MnMLO12B clustered with functionally characterized MLOs associated with powdery mildew susceptibility in dicot species. Gene expression analysis indicated increased transcript abundance of MnMLO2, MnMLO6A, and MnMLO12A in response to powdery mildew infection. Further, conserved motifs exclusive to functionally characterized MLOs were identified in MnMLO1C, MnMLO2 and MnMLO6A proteins. Combined analysis of the phylogenetic relationship, conserved motif analysis and gene expression in response to infection identified MnMLO2 and MnMLO6A as potential candidate genes involved in powdery mildew susceptibility in mulberry. Identification and deployment of natural and induced mutations in the candidate genes can be useful for mulberry breeding programs to develop powdery mildew resistant varieties.

Selection of suitable reference genes for quantitative real-time PCR gene expression analysis in Mulberry (Morus alba L.) under different abiotic stresses.

Mulberry (Morus alba L.) is the sole food source for the mulberry silkworm, Bombyx mori and therefore important for sericulture industry. Different abiotic stress conditions like drought, salt, heat and cold stress adversely affect the productivity and quality of mulberry leaves. Quantitative real time PCR (qPCR) is a reliable and widely used method to identify abiotic stress responsive genes and molecular mechanism in different plant species. Selection of suitable reference genes is important requirement for normalizing the expression of genes through qRT-PCR study. In the present study, we have selected eight candidate reference genes in mulberry for analyzing their expression stability in different abiotic stress treatments including drought, salt, heat and cold stresses. The expression stability of these reference genes was determined using geNorm, NormFinder and RefFinder statistical algorithms. The results showed that Ubiquitin and protein phosphatase 2A regulatory subunit A (PP2A) were the most stable genes across all the treatment samples. However, analysis of individual stresses revealed different expression profiles and stability of reference genes. Actin3 and PP2A were most stable in drought and salt conditions respectively. RPL3 most preferred in heat stress and Ubiquitin was most stable in cold stress. We propose the ubiquitin and PP2A are the preferred reference genes for normalization of gene expression data from abiotic stresses. In addition, Actin3 are preferred for drought stress, PP2A for salt stress, RPL3 for heat stress and Ubiquitin for cold stress studies.

Transcriptomics and functional genomics of ROS-induced cell death regulation by RADICAL-INDUCED CELL DEATH1.

Plant responses to changes in environmental conditions are mediated by a network of signaling events leading to downstream responses, including changes in gene expression and activation of cell death programs. Arabidopsis thaliana RADICAL-INDUCED CELL DEATH1 (RCD1) has been proposed to regulate plant stress responses by protein-protein interactions with transcription factors. Furthermore, the rcd1 mutant has defective control of cell death in response to apoplastic reactive oxygen species (ROS). Combining transcriptomic and functional genomics approaches we first used microarray analysis in a time series to study changes in gene expression after apoplastic ROS treatment in rcd1. To identify a core set of cell death regulated genes, RCD1-regulated genes were clustered together with other array experiments from plants undergoing cell death or treated with various pathogens, plant hormones or other chemicals. Subsequently, selected rcd1 double mutants were constructed to further define the genetic requirements for the execution of apoplastic ROS induced cell death. Through the genetic analysis we identified WRKY70 and SGT1b as cell death regulators functioning downstream of RCD1 and show that quantitative rather than qualitative differences in gene expression related to cell death appeared to better explain the outcome. Allocation of plant energy to defenses diverts resources from growth. Recently, a plant response termed stress-induced morphogenic response (SIMR) was proposed to regulate the balance between defense and growth. Using a rcd1 double mutant collection we show that SIMR is mostly independent of the classical plant defense signaling pathways and that the redox balance is involved in development of SIMR.

Neuroprotective effects of bikaverin on H2O2-induced oxidative stress mediated neuronal damage in SH-SY5Y cell line.

The generation of free radicals and oxidative stress has been linked to several neurodegenerative diseases including Parkinson's disease, Alzheimer's disease, Huntington's disease, and Amyotrophic lateral sclerosis. The use of free radical scavenging molecules for the reduction of intracellular reactive oxygen species is one of the strategies used in the clinical management of neurodegeneration. Fungal secondary metabolism is a rich source of novel molecules with potential bioactivity. In the current study, bikaverin was extracted from Fusarium oxysporum f. sp. lycopersici and its structural characterization was carried out. Further, we explored the protective effects of bikaverin on oxidative stress and its anti-apoptotic mechanism to attenuate H2O2-induced neurotoxicity using human neuroblastoma SH-SY5Y cells. Our results elucidate that pretreatment of neurons with bikaverin attenuates the mitochondrial and plasma membrane damage induced by 100 µM H2O2 to 82 and 26% as evidenced by MTT and LDH assays. H2O2 induced depletion of antioxidant enzyme status was also replenished by bikaverin which was confirmed by Realtime Quantitative PCR analysis of SOD and CAT genes. Bikaverin pretreatment efficiently potentiated the H2O2-induced neuronal markers, such as BDNF, TH, and AADC expression, which orchestrate the neuronal damage of the cell. The H2O2-induced damage to cells, nuclear, and mitochondrial integrity was also restored by bikaverin. Bikaverin could be developed as a preventive agent against neurodegeneration and as an alternative to some of the toxic synthetic antioxidants.

RCD1-DREB2A interaction in leaf senescence and stress responses in Arabidopsis thaliana.

Transcriptional regulation of gene expression is one major determinant of developmental control and stress adaptation in virtually all living organisms. In recent years numerous transcription factors controlling various aspects of plant life have been identified. The activity of transcription factors needs to be regulated to prevent unspecific, prolonged or inappropriate responses. The transcription factor DREB2A (DEHYDRATION-RESPONSIVE ELEMENT BINDING 2A) has been identified as one of the main regulators of drought and heat responses, and it is regulated through protein stability. In the present paper we describe evidence that the interaction with RCD1 (RADICAL-INDUCED CELL DEATH 1) contributes to the control of DREB2A under a range of conditions. The interaction is mediated by a novel protein motif in DREB2A and a splice variant of DREB2A which lacks the interaction domain accumulates during heat stress and senescence. In addition RCD1 is rapidly degraded during heat stress, thus our results suggest that removal of RCD1 protein or the loss of the interaction domain in DREB2A appears to be required for proper DREB2A function under stress conditions.

Flunarizinium hydrogen maleate.

In the cation of the title salt {systematic name: 4-[bis-(4-fluoro-phen-yl)meth-yl]-1-[(2E)-3-phenyl-prop-2-en-1-yl]piperazin-1-ium hydrogen maleate}, C26H27F2N2 (+)·C4H3O4 (-), the protonated piperazine ring is in a chair conformation. The dihedral angle between the 4-fluoro-phenyl rings is 68.2 (2)°. An intra-molecular O-H⋯O hydrogen bond occurs in the anion. In the crystal, N-H⋯O, C-H⋯O and C-H⋯F inter-actions are observed, which link the ions into [001] chains.

(E)-5-(2-Chloro-phen-yl)-7-ethyl-2-oxo-2,3-dihydro-1H-thieno[2,3-e][1,4]diazepin-4-ium 2,4,6-trinitro-phenolate.

In the title molecular salt, C(15)H(14)ClN(2)OS(+)·C(6)H(2)N(3)O(7) (-), protonation occurred on the double-bonded N atom. One of the nitro groups shows slight disorder over two orientations, with an occupancy ratio of 0.91:0.09. In the crystal, classical N-H⋯O hydrogen bonds, as well as C-H⋯O contacts connect the components into a three-dimensional network. The seven-membered ring adopts a boat-like conformation. The least-squares plane defined by its non-H atoms encloses an angle of 38.99 (6)° with the benzene ring bonded to it.

Redetermination of loperamide monohydrate.

The structure of the title compound {systematic name: 4-[4-(4-chloro-phen-yl)-4-hy-droxy-piperidin-1-yl]-N,N-dimethyl-2,2-di-phenyl-butanamide monohydrate}, C(29)H(33)ClN(2)O(2)·H(2)O, has been redetermined at 170 (2) K. The redetermination is of significantly higher precision than the previous structure determination at room temperature and includes the H-atom coordinates that were not included in the previous report [Germain et al. (1977 ▶). Acta Cryst. B33, 942-944]. It consists of a piperidin-1-yl ring in a distorted chair conformation, with the N,N-dimethyl-α,α-diphenyl-butyramide and the 4-chloro-phenyl and hy-droxy groups bonded in para positions and an external water mol-ecule within the asymmetric unit. The dihedral angles between the mean plane of the piperidine ring and the 4-chloro-phenyl and two benzene rings are 83.4 (5), 76.4 (2) and 85.9 (2)°, respectively. The two benzene rings are inclined to one another by 50.8 (6)°. In the crystal, mol-ecules are linked by O-H⋯O and O-H⋯N hydrogen bonds and weak C-H⋯O intermolecular interactions, forming an infinite two-dimensional network along [110].

2-Amino-N-[3-(2-chloro-benzo-yl)-5-ethyl-thio-phen-2-yl]acetamide.

In the title compound, C(15)H(15)ClN(2)O(2)S, the 2-amino-acetamide N-C(=O)-C-N unit is approximately planar, with an r.m.s. deviation of 0.020 (4) Å. The central thio-phene ring makes dihedral angles of 7.84 (11) and 88.11 (11)°, respectively, with the 2-amino-acetamide unit and the 2-chloro-phenyl ring. An intra-molecular N-H⋯O hydrogen bond generates an S(6) ring motif. In the crystal, mol-ecules are linked by an N-H⋯O hydrogen bond and weak C-H⋯O inter-actions into a chain along the c axis. A C-H⋯π inter-action is also present.

Methyl 2,2-diphenyl-2-(prop-2-yn-1-yl-oxy)acetate.

The mol-ecular structure of the title compound, C(18)H(16)O(3), exhibits a new R(2)-C(COOMe)(OCH(2)CCH) group. The C-O-C-C torsion angle is 153.3 (1)°. The dihedral angles are 79.89 (5)° between phen-yl/phenyl planes, and 73.13 (5) and 79.05 (8)° for the two COOMe/phenyl plane pairs.

1-[Bis(4-fluoro-phen-yl)meth-yl]piperazine.

In the title mol-ecule, C(17)H(18)F(2)N(2), the dihedral angle between the benzene rings is 73.40 (3)°. The piperazine ring is close to an ideal chair conformation and the N-H hydrogen is in an equatorial position. In the crystal, molecules are linked via weak C-H⋯F hydrogen bonds.

3,3-Dimethyl-2-benzofuran-1(3H)-one.

In the title compound, C(10)H(10)O(2), all the non-H atoms except the methyl C atoms lie on a crystallographic mirror plane. In the crystal, C-H⋯O hydrogen bonds link the mol-ecules into zigzag chains running parallel to [100]. Weak π-π stacking inter-actions between the benzene rings [centroid-centroid distance = 3.9817 (5) Å] link the chains in the [010] direction.

Amylase production by endophytic fungi Cylindrocephalumsp. isolated from medicinal plant Alpinia calcarata (Haw.) Roscoe.

Amylases are among the most important enzymes used in modern biotechnology particularly in the process involving starch hydrolysis. Fungal amylase has large applications in food and pharmaceutical industries. Considering these facts, endophytic fungi isolated from the plant Alpinia calcarata (Haw.) Roscoe were screened for amylolytic activity on glucose yeast extract peptone agar (GYP) medium. Among thirty isolates of endophytic fungi, isolate number seven identified as Cylindrocephalum sp. (Ac-7) showed highest amylolytic activity and was taken for further study. Influence of various physical and chemical factors such as pH, temperature, carbon and nitrogen sources on amylase production in liquid media were studied. The maximal amylase production was found to be at 30(º)C and at pH 7.0 of the growth medium. Among the various carbon and nitrogen sources tested, maltose at 1.5% and Sodium nitrate at 0.3% respectively gave optimum amylase production.

2-(2-Benzyl-phen-yl)propan-2-ol.

There are two mol-ecules in the asymmetric unit of the title compound, C(16)H(18)O, a tertiary alcohol featuring a 2-benzyl-phenyl substituent. Co-operative O-H⋯O hydrogen bonds connect the mol-ecules into tetra-mers.

Unequally redundant RCD1 and SRO1 mediate stress and developmental responses and interact with transcription factors.

RADICAL-INDUCED CELL DEATH1 (RCD1) is an important regulator of stress and hormonal and developmental responses in Arabidopsis thaliana. Together with its closest homolog, SIMILAR TO RCD-ONE1 (SRO1), it is the only Arabidopsis protein containing the WWE domain, which is known to mediate protein-protein interactions in other organisms. Additionally, these two proteins contain the core catalytic region of poly-ADP-ribose transferases and a conserved C-terminal domain. Tissue and subcellular localization data indicate that RCD1 and SRO1 have partially overlapping functions in plant development. In contrast mutant data indicate that rcd1 has defects in plant development, whereas sro1 displays normal development. However, the rcd1 sro1 double mutant has severe growth defects, indicating that RCD1 and SRO1 exemplify an important genetic principle - unequal genetic redundancy. A large pair-wise interaction test against the REGIA transcription factor collection revealed that RCD1 interacts with a large number of transcription factors belonging to several protein families, such as AP2/ERF, NAC and basic helix-loop-helix (bHLH), and that SRO1 interacts with a smaller subset of these. Full genome array analysis indicated that in many cases targets of these transcription factors have altered expression in the rcd1 but not the sro1 mutant. Taken together RCD1 and SRO1 are required for proper plant development.

The RST and PARP-like domain containing SRO protein family: analysis of protein structure, function and conservation in land plants.

BACKGROUND: The SROs (SIMILAR TO RCD-ONE) are a group of plant-specific proteins which have important functions in stress adaptation and development. They contain the catalytic core of the poly(ADP-ribose) polymerase (PARP) domain and a C-terminal RST (RCD-SRO-TAF4) domain. In addition to these domains, several, but not all, SROs contain an N-terminal WWE domain. RESULTS: SROs are present in all analyzed land plants and sequence analysis differentiates between two structurally distinct groups; cryptogams and monocots possess only group I SROs whereas eudicots also contain group II. Group I SROs possess an N-terminal WWE domain (PS50918) but the WWE domain is lacking in group II SROs. Group I domain structure is widely represented in organisms as distant as humans (for example, HsPARP11). We propose a unified nomenclature for the SRO family. The SROs are able to interact with transcription factors through the C-terminal RST domain but themselves are generally not regulated at the transcriptional level. The most conserved feature of the SROs is the catalytic core of the poly(ADP-ribose) polymerase (PS51059) domain. However, bioinformatic analysis of the SRO PARP domain fold-structure and biochemical assays of AtRCD1 suggested that SROs do not possess ADP-ribosyl transferase activity. CONCLUSIONS: The SROs are a highly conserved family of plant specific proteins. Sequence analysis of the RST domain implicates a highly preserved protein structure in that region. This might have implications for functional conservation. We suggest that, despite the presence of the catalytic core of the PARP domain, the SROs do not possess ADP-ribosyl transferase activity. Nevertheless, the function of SROs is critical for plants and might be related to transcription factor regulation and complex formation.

Desipramine hydro-chloride: a non-merohedrally twinned structure.

The title compound, C(18)H(23)N(2) (+)·Cl(-), is a non-merohedrally twinned salt [domains 0.9288 (3) and 0.0712 (3)] which crystallizes with four independent cation-anion pairs in the asymmetric unit. The seven-membered ring in each of the cations adopts a boat conformation, thus creating a butterfly effect within the ring system. The average value of the dihedral angle between the two aromatic rings in the four cations is 57.1 (1)°. The crystal packing is stabilized only slightly by a collection of inter-mediate N-H⋯Cl hydrogen-bonding inter-actions, which produce a weak, but cooperative, infinite, one-dimensional, inter-molecular hydrogen-bond network along the a axis. A MOPAC PM3 computational calculation gives support to these observations.

Levocetirizinium dipicrate.

There are two cation-dianion pairs in the asymmetric unit of the title compound, C(21)H(27)ClN(2)O(3) (2+)·2C(6)H(2)N(3)O(7) (-) {systematic name: 1-[2-(carb-oxy-meth-oxy)eth-yl]-4-[(R)-(4-chloro-phen-yl)phenyl-meth-yl]piperazine-1,4-diium bis-(2,4,6-trinitro-phenol-ate)}. The piperazine group in the levocetirizinium cation is protonated at both N atoms. The acetyl end groups form R(2) (2)(8) hydrogen-bonded motifs with adjacent cations. Each picrate anion inter-acts with the proponated N atom in the cation through a bifurcated N-H⋯O hydrogen bond, forming R(1) (2)(6) ring motifs. Strong and weak inter-molecular N-H⋯O and strong O-H⋯O hydrogen bonds, and weak π-ring and π-π stacking inter-actions [centroid-centroid distance = 3.7419 (14) Å] dominate the crystal packing, creating a three-dimensional supra-molecular structure.