Patterns of alien plant diversity in the urban landscapes of global biodiversity hotspots: a case study from the Himalayas

In an age of Anthropocene, the urban landscapes are recognised as the ‘hotspots’ of human-mediated alien species introductions. As the cities provide an ideal natural experimental system to investigate the patterns of alien plant diversity in urban landscapes, the present study aimed to unravel the taxonomic, biogeographic and ecological patterns of alien flora of Srinagar—one of the largest urban centres in the Himalayan biodiversity hotspot. The alien flora of Srinagar comprises 325 species, constituting ca.35% of total flora of the city. Out of the 325 alien species documented, 157 species (43%) were recorded to be under cultivation, while 168 species (57%) were growing in the wild (i.e., outside cultivation); those growing in the wild, in turn, comprised 110 cultivation escapes and 58 accidentally introduced plant species. Biogeographically, two-third of the alien plant diversity reported from Srinagar is native to Asia-Temperate. This indicates that climatic similarity between Asia-Temperate and Kashmir Himalayas facilitate in flourishing similar floristic diversity. The study highlights a relatively higher proportion of herbaceous growth form in the aliens growing in the wild (80%) than those under cultivation (43%). Similarly, 82% of the alien species under cultivation had a perennial life span, but those growing in the wild were dominated by annuals (44%). Currently, 45 species are growing as casuals and 124 species are naturalised (including 105 naturalised non-invasive and 19 naturalised invasive). Along the continuum of casual-naturalised-invasive categories, the contribution of cultivation escapes and accidently introduced aliens contrastingly shows decreasing and increasing trends respectively. Interestingly, the results revealed that the human practice of stopping cultivation of alien escapes increased rapidly as we move along the continuum. Thus, the present study has investigated the patterns of alien plant diversity in the urban landscape of Srinagar, and the results obtained offer scientific insights toward better scientific understanding and management of plant invasions in this Himalayan city, with wider policy implications for neighbouring urbanised landscapes in the Himalayas and other mountainous regions across the world.     

Rapid virulence prediction and identification of Newcastle disease virus genotypes using third-generation sequencing

Background

Newcastle disease (ND) outbreaks are global challenges to the poultry industry. Effective management requires rapid identification and virulence prediction of the circulating Newcastle disease viruses (NDV), the causative agent of ND. However, these diagnostics are hindered by the genetic diversity and rapid evolution of NDVs.

Methods

An amplicon sequencing (AmpSeq) workflow for virulence and genotype prediction of NDV samples using a third-generation, real-time DNA sequencing platform is described here. 1D MinION sequencing of barcoded NDV amplicons was performed using 33 egg-grown isolates, (15 NDV genotypes), and 15 clinical swab samples collected from field outbreaks. Assembly-based data analysis was performed in a customized, Galaxy-based AmpSeq workflow. MinION-based results were compared to previously published sequences and to sequences obtained using a previously published Illumina MiSeq workflow.

Results

For all egg-grown isolates, NDV was detected and virulence and genotype were accurately predicted. For clinical samples, NDV was detected in ten of eleven NDV samples. Six of the clinical samples contained two mixed genotypes as determined by MiSeq, of which the MinION method detected both genotypes in four samples. Additionally, testing a dilution series of one NDV isolate resulted in NDV detection in a dilution as low as 10¹ 50% egg infectious dose per milliliter. This was accomplished in as little as 7 min of sequencing time, with a 98.37% sequence identity compared to the expected consensus obtained by MiSeq.

Conclusion

The depth of sequencing, fast sequencing capabilities, accuracy of the consensus sequences, and the low cost of multiplexing allowed for effective virulence prediction and genotype identification of NDVs currently circulating worldwide. The sensitivity of this protocol was preliminary tested using only one genotype. After more extensive evaluation of the sensitivity and specificity, this protocol will likely be applicable to the detection and characterization of NDV.

     

Identification and Characterization of Novel Antimicrobial Peptide from <Emphasis Type="Italic">Hippocampus comes</Emphasis> by In Silico and Experimental Studies

Antimicrobial peptides (AMPs) have attracted attentions as a novel antimicrobial agent because of their unique activity against microbes. In the present study, we described a new, previously unreported AMP, moronecidin-like peptide, from Hippocampus comes and compared its antimicrobial activity with moronecidin from hybrid striped bass. Antibacterial assay indicated that gram-positive bacteria were more sensitive to moronecidin and moronecidin-like compared with gram-negative bacteria. Furthermore, both AMPs were found to exhibit effective antifungal activity. Comparative analysis of the antimicrobial activity revealed that moronecidin-like peptide has higher activity against Acinetobacter baumannii and Staphylococcus epidermidis relative to moronecidin. Both moronecidin-like and moronecidin peptides retained their antibacterial activity in physiological pH and salt concentration. The time-killing assay showed that the AMPs completely killed A. baumannii and S. epidermidis isolates after 1 and 5 h at five- and tenfold above their corresponding MICs, respectively. Anti-biofilm assay demonstrated that peptides were able to inhibit 50% of biofilm formation at sub-MIC of 1/8 MIC. Furthermore, moronecidin-like significantly inhibited biofilm formation more than moronecidin at 1/16 MIC. Collectively, our results revealed that antimicrobial and anti-biofilm activities of moronecidin-like are comparable to moronecidin. In addition, the hemolytic and cytotoxic activities of moronecidin-like were lower than those of moronecidin, suggesting it as a potential novel therapeutic agent, and a template to design new therapeutic AMPs.     

Effects of Increased Salinity on Growth,Development and Survival in Early Life Stages of the Green Toad Bufotes variabilis (Anura: Bufonidae)

This study examined the effects of increased salinity on growth,development and survival of the Green toad,Bufotes variabilis during embryonic,hatching and early larval periods.Eggs from a single cohort of B.variabilis were subjected to acute and chronic toxicity tests for water salinity ranging from 0.20 to 10 g of salt per liter.Results obtained from this study showed that salinity over 3.70 g/l increased embryonic mortality and reduced percentage of hatching and survival rate of larvae.As larvae tolerated salinity 0.20 to 3.70 g/l with highest survival,but salinity of 10 g/l caused mortality of all individuals within 12 h,7.70–8.70(g/l)within 4.5 days,5.70–6.70 g/l within 10 days and 4.70(g/l)were tolerated within 14 days.Salinity less than 0.70 g/l did not affect survival and hatching success of the embryos.After a 3-week experiment,size of larvae exposed to salinities over 0.70 g/l was lower compared to larvae reared at lower salinity levels.Meanwhile increases in salinity more than 3.70 g/l caused extension in the hatching period.Larvae reared at salinity of 3.70 to 4.70 g/l had morphological abnormalities,such as distortion of tail.     

Interaction of iron nanoparticles with nervous system: an in vitro study

Nanoparticles (NPs) are one of the interesting and widely studying issues mainly because of their particular physico-chemical features and broad applications in the field of biomedical sciences, such as diagnosis and drug delivery. In this study, the interaction of iron nanoparticles (Fe–NPs) with Tau protein and PC12 cell, as potential nervous system models, was investigated with a range of techniques including dynamic light scattering, intrinsic fluorescence spectroscopy, circular dichroism, [(3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-tetrazolium-bromid] assay, and acridine orange/ethidium bromide (AO/EB) dual staining method. An inverse correlation between Stern and Volmer constant (K_SV) and temperature indicated a probable static quenching mechanism occurred between Tau protein and Fe–NPs. The number of binding site (n = 0.86) showed that there is almost one binding site of Fe–NP per protein. The negative values of ?H (?53.21 kJ/mol) and T?S (?42.44 kJ/mol) revealed that Fe–NPs interacts with Tau protein with dominate role of hydrogen bonds and van der Waals interactions and this interaction was spontaneous (?G = ?10.77 kJ/mol). Also, Fe–NPs stabilized the random coil structure of Tau protein. Moreover, Fe–NPs reduced PC12 cells viability by fragmentation of DNA in an apoptotic manner. In conclusion, induced conformational changes of Tau protein and cytotoxicity of PC12 cells by Fe–NP were revealed to be in a concentration and time-dependent manner.     

Random Motion of Chromatin Is Influenced by Lamin A Interconnections

Using fluorescence correlation spectroscopy in single-plane illumination microscopy, we investigated the dynamics of chromatin in interphase mouse adult fibroblast cell nuclei under the influence of the intermediate filament protein lamin A. We find that 1) lamin A-eGFP and histone H2A-mRFP show significant comobility, indicating that their motions are clearly interconnected in the nucleus, and 2) that the random motion of histones H2A within the chromatin network is subdiffusive, i.e., the effective diffusion coefficient decreases for slow timescales. Knocking out lamin A changes the diffusion back to normal. Thus, lamin A influences the dynamics of the entire chromatin network. Our conclusion is that lamin A plays a central role in determining the viscoelasticity of the chromatin network and helping to maintain local ordering of interphase chromosomes.     

Upregulation of selective cholesteryl ester uptake pathway in mice with deletion of low-density lipoprotein receptor function

This study examines the effect of mutation of the low-density lipoprotein receptor (LDLR) on cholesterol metabolism, and especially lipoprotein-derived cholesteryl ester uptake, in murine ovarian granulosa cells. Although the tests were conducted on cells prepared by two different procedures, the results are similar. Deletion of LDLR function did not noticeably affect key enzymes of the steroidogenic pathway or affect progestin production and secretion in granulosa cells. No change was found in expression of LDL-related protein (LRP). These data suggested that cholesterol turnover in cells from the knockout animals is within normal limits and that the cells are not stressed to acquire more cholesterol. Both biochemical and morphological data indicate that unstimulated granulosa cells from LDLR^−/− mice are nonetheless programmed to take in double the amount of lipoprotein-derived cholesteryl ester (via the selective cholesteryl ester uptake pathway) and to process (hydrolyze, re-esterify, or utilize) more than twofold the cholesteryl ester processed by cells from wildtype (LDLR^+/+) animals. Bt₂cAMP stimulation of the murine granulosa cells increases the mass of cholesteryl ester taken up by the selective pathway by an additional 38%. To determine to what extent this increase is related to high-density lipoprotein (HDL) scavenger receptor protein (SR-BI) or caveolin function, Western blots and immunohistochemical studies were performed under a variety of conditions. SR-BI levels are found to be low in unstimulated cells of both LDLR^+/+ and LDLR^−/− animals, but highly expressed (∼20-fold increase over basal levels) in stimulated (Bt₂cAMP) cells of both animal models. Thus, the functional relationship between selective cholesteryl ester uptake and SR-BI receptor protein is not as tight as in previously reported studies, suggesting a requirement for other tissue factors. Caveolin expression did not change under any of the conditions tested and appears not to be functionally involved in this process. J. Cell. Physiol. 180:190–202, 1999. Published 1999 Wiley-Liss, Inc.