Mitochondrial Genome of Episesarma lafondii(Brachyura:Sesarmidae)and Comparison with Other Sesarmid Crabs

Complete mitochondrial genomes(mitogenomes)can provide useful information for phylogenetic relationships,gene rearrangement,and molecular evolution.Here,the complete mitogenome of Episesarma lafondii(Brachyura:Grapsoidea:Sesarmidae)was sequenced through next-generation sequencing technique for the first time.The 15640 bp mitogenome contains the entire set of 37 genes and an AT-rich region.The rearrangements of two tRNA genes(tRNA-His and tRNA-Gln)are compared with that in the pancrustacean ground pattern,and the tandem duplication/random loss model was selected to explain the observed gene rearrangements.The phylogenetic results showed that all sesarmid crabs belong to the same group,wherein the genus Episesarma showed the closest relationship with Clistocoeloma.Furthermore,the monophyly of each family was well supported except for Xanthidae,Gecarcinidae,and Homolidae.The correlation between the phylogeny of Sesarmidae species and the gaps in the QIM region was analyzed.Evidently,the gaps between Q and I(Gap3 and between I and M(Gap4)degenerated with the evolution process.In general,the results will contribute to the in-depth understanding of gene rearrangements in Sesarmidae mitogenomes and provide new insights into the phylogeny of Brachyura.

Comparative mitochondrial genome analysis of Varunidae and its phylogenetic implications

Complete mitochondrial genomes(mitogenomes)can indicate phylogenetic relationships,as well as useful information for gene rearrangement mechanisms and molecular evolution.Currently,the phylogenetic location of the genus Varuna(Brachyura:Varunidae)has not been well resolved mainly because of limited representatives(only two extant species).Here,we determined a new mitogenome of this genus(Varuna litterata)and added the published mitogenomes to reconstruct the phylogeny of Varunidae.The 16368-bp mitogenome contains the entire set of 37 genes and a putative control region.The characteristics of this newly sequenced mitogenome were described and compared with the other 15 Varunidae mitogenomes.All 16 analyzed mitogenomes have identical gene order and similar molecular features.The sliding window and genetic distance analyses demonstrate highly variable nucleotide diversity,with comparatively low variability of COI and COII,and high variability of ND6.The nonsynonymous/synonymous substitution rates(dN/dS ratio)analysis shows that all 13 PCGs are under purifying selection and ATP8 gene evolves under the least selective pressure.Twelve tRNA genes,two rRNAs,one PCG,and the putative control region are found to be rearranged with respect to the pancrustacean ground pattern gene order.Tandem duplication/random loss model is adopted to explain the large-scale gene rearrangement events occurring in Varunidae mitogenomes.Phylogenetic analyses show that all Varunidae species are placed into one group,and form a sister clade with Macrophthalmidae.Nevertheless,the phylogenetic relationships within Varunidae are not completely consistent based on the two different datasets used in this study.These findings will contribute to a better understanding of gene rearrangement and molecular evolution in Varunidae mitogenomes,as well as provide insights into the phylogenetic studies of Brachyura.

Combination of multi-focus Raman spectroscopy and compressive sensing for parallel monitoring of single-cell dynamics

To overcome the low efficiency of conventional confocal Raman spectroscopy,many efforts have been devoted to parallelizing the Raman excitation and acquisition,in which the scattering from multiple foci is projected onto different locations on a spectrometer's CCD,along either its vertical,horizontal dimension,or even both.While the latter projection scheme relieves the limitation on the row numbers of the CCD,the spectra of multiple foci are recorded in one spectral channel,resulting in spectral overlapping.Here,we developed a method under a com-pressive sensing framework to demultiplex the superimposed spectra of multiple cells during their dynamic processes.Unlike the previous methods which ignore the information connection be-tween the spectra of the cells recorded at different time,the proposed method utilizes a prior that a cell's spectra acquired at different time have the same sparsity structure in their principal components.Rather than independently demultiplexing the mixed spectra at the individual time intervals,the method demultiplexes the whole spectral sequence acquired continuously during the dynamic process.By penalizing the sparsity combined from all time intervals,the collaborative optimization of the inversion problem gave more accurate recovery results.The performances of the method were substantiated by a 1D Raman tweezers array,which monitored the germination of multiple bacterial spores.The method can be extended to the monitoring of many living cells randomly scattering on a coverslip,and has a potential to improve the throughput by a few orders.

Potentials of marine natural products against malaria, leishmaniasis, and trypanosomiasis parasites: a review of recent articles

Background:Malaria and neglected communicable protozoa parasitic diseases,such as leishmaniasis,and trypanosomiasis,are among the otherwise called diseases for neglected communities,which are habitual in underprivileged populations in developing tropical and subtropical regions of Africa,Asia,and the Americas.Some of the currently available therapeutic drugs have some limitations such as toxicity and questionable efficacy and long treatment period,which have encouraged resistance.These have prompted many researchers to focus on fin ding new drugs that are safe,effective,and affordable from marine environ merits.The aim of this review was to show the diversity,structural scaffolds,in-vitro or in-vivo efficacy,and recent progress made in the discovery/isolation of marine natural products(MNPs)with potent bioactivity against malaria,leishmaniasis,and trypanosomiasis.Main text:We searched PubMed and Google scholar using Boolean Operators(AND,OR,and NOT)and the combination of related terms for articles on marine natural products(MNPs)discovery published only in English language from January 2016 to June 2020.Twenty nine articles reported the isolation,identification and antiparasitic activity of the isolated compounds from marine environment.A total of 125 compounds were reported to have been isolated,out of which 45 were newly isolated compounds.These compounds were all isolated from bacteria,a fungus,sponges,algae,a bryozoan,cnidarians and soft corals.In recent years,great progress is being made on anti-malarial drug discovery from marine organisms with the isolation of these potent compounds.Comparably,some of these promising antikinetoplastid MNPs have potency better or similar to conventional drugs and could be developed as both antileishmanial and antitrypanosomal drugs.However,very few of these MNPs have a pharmaceutical destiny due to lack of the following:sustainable production of the bioactive compounds,stan da rd efficient screening methods,knowledge of the mechanism of action,partnerships between researchers and pharmaceutical industries.Conclusions:It is crystal clear that marine organisms are a rich source of antiparasitic compounds,such as alkaloids,terpenoids,peptides,polyketides,terpene,coumarins,steroids,fatty acid derivatives,and lactones.The current and future technological innovation in natural products drug discovery will bolster the drug armamentarium for malaria and neglected tropical diseases.

Optimization of the in-situ growth conditions based on a novel photo-microcalorimeter for the sustainable cultivation of photosynthetic microorganisms

Despite the great potential of photosynthetic microbes in the production of renewable fuels,value-adding chemicals,and water treatment,etc.,commercial utilization of them is significantly hindered by the lack of techniques to accurately monitor the thermodynamic and kinetic characteristics of the in-situ growth of microbes under controlled light illumination for optimal cultivation.Herein,we demonstrated that a newly developed highly sensitive photo-microcalorimetric system successfully captured the impacts of the light wavelength and strength on the thermodynamic and kinetic parameters of the in-situ growth of Rhodopseudomonas palustris,a representative photosynthetic microorganism.To our best knowledge,this is the first time that highly precise microcalorimetry is employed to monitor exam the in-situ growth of photosynthetic microorganisms under controllable photo illumination.We envision this technique can help for the optimization of the growth conditions of photosynthetic microorganisms for scale-up applications.

The Streptococcus agalactiae Ribose Binding Protein B (RbsB) Mediates Quorum Sensing Signal Uptake via Interaction with Autoinducer-2 Signals

Understanding aquatic pathogen in sediments or aquacultural water is crucial to protect public health from soilborne and waterborne diseases.Quorum sensing(QS)was increasingly reported in biological wastewater treatment processes because of their inherent roles in biofilm development,bacterial aggregation and so on.The widely QS signals was Antoinducer-2(AI-2),primarily involved to allow the possibility of interspecies communication.However,the cellular components that mediate the response of Streptococcus agalactiae to AI-2 have not been fully characterized.Analysis of the complete genome sequence of S.agalactiae indi-cated that its RbsB protein has similarity to Escherichia coli LsrB and Aggregatibacter actinomycetemcomitans RbsB proteins that bind AI-2.We hypothesized that RbsB protein mediates quorum sensing signal uptake via interaction with AI-2.To evaluate the regulatory effect of RbsB on QS system,the recombinant plasmid pGEX-6p-1-RbsB was constructed and RbsB protein was purified with GST-tag.To further elucidate the role of RbsB protein binding to DPD(AI-2 precursor dihydroxypentanedione),the systemati-cally throughput circular dichroism(CD)spectroscopy,isothermal titration calorimetry200(ITC200)and molecular docking methods were employed.The high expression of soluble RbsB protein with molecular weight of 33 kDa was obtained.The thermodynamics results(ΔH<0,ΔS<0,ΔG<0)with ITC determination indicated that the binding process between DPD and RbsB was exothermic and spontaneous,with hydrogen bonds and van der Waals forces as the main binding forces.Obviously,DPD can be more easily combined with RbsB in a dose-dependent manner,suggesting that RbsB was changed in the microenvironment of DPD when the DPD concentration was between 0.8-1.0mmolL−1 and reaching the maximum binding amount.According to molecular docking,3 hydrophobic residues involved in DPD and RbsB protein stable binding were be found,and also hydrogen bonding plays a key role in the formation of the new complex.RbsB efficiently inhibited V.harveyi bioluminescence induced by both S.agalactiae AI-2 and V.harveyi AI-2 in a dose-dependent manner.However,our results suggest that RbsB may play a role in the response of S.agalactiace to AI-2.