Deciphering the global phylogeography of a coastal shrub (Scaevola taccada) reveals the influence of multiple forces on contemporary population structure

The phylogeography of coastal plant species is heavily influenced by past sealevel fluctuations, dispersal barriers, and life-history traits, such as long-distance dispersal ability of the propagules. Unlike the widely studied mangroves, phylogeographic patterns have remained mostly obscure for other coastal plant species. In this study, we sampled 42 populations of Scaevola taccada (Gaertn.) Roxb., a coastal shrub of the family Goodeniaceae, from 17 countries across its distribution range. We used five chloroplast DNA (cpDNA) and 14 nuclear microsatellite (simple sequence repeat [SSR]) markers to assess the influence of abiotic factors and population genetic processes on the phylogeographic pattern of the species. Geographical distribution of cpDNA haplotypes suggests that the species originated in Australia, followed by historical dispersal and expansion of its geographic range. Multiple abiotic factors, including the sealevel changes during the Pleistocene, the presence of landmasses like the Malay Peninsula, and contemporary oceanic circulation patterns, restricted gene flow between geographically distinct populations, thereby creating low haplotype diversity and a strong population structure. Population genetic processes acted on these isolated populations, leading to high nuclear genetic diversity and population differentiation, as revealed from analyzing the polymorphic SSR loci. Although genetic divergence was mostly concordant between cpDNA and SSR data, asymmetrical gene flow and ancestral polymorphism could explain the discordance in the detailed genetic structure. Overall, our findings indicate that abiotic factors and population genetic processes interactively influenced the evolutionary history and current phylogeographic pattern of S. taccada across its distribution range.     

Light from heat lamps affects sow behaviour and piglet salivary melatonin levels

The light environment regulates animal physiology and behaviour. As widely used supplementary heat sources in creep areas, the effect of visible light radiated by infrared heat lamps on pigs is worth investigating. To investigate the effects of light from heat lamps on the behaviour of sows and piglets and possible endocrine mechanisms, 24 primiparous sows were randomly assigned to three supplementary heat source treatments: (1) 250 W non-luminous ceramic heat lamps (CE, n = 8), (2) 175 W red heat lamps (RL, n = 8), and (3) 175 W transparent heat lamps (TL, n = 8). All heat lamps were turned off on Day 15 postpartum. Piglets were weighed on days 3 and 21 postpartum. The number and duration of suckling within 24 h were analysed via video recordings on days 4, 8, and 16 postpartum. Sow posture changes during the day and night were detected using the YOLOv4 target detection network model. One marked piglet from six litters randomly selected from each treatment was used for saliva collection. Saliva samples were collected at 0800, 1400, 2000, and 0200 (+1 d) on days 10 and 20 postpartum. The results showed that the mean postural change frequency of TL sows was higher than that of CE sows (P < 0.05), while that of RL sows was not different from that of CE and TL sows. However, the duration of the sows being in each posture was not affected by the treatment. The total suckling duration of TL piglets was significantly longer than that of CE piglets, but there was no significant difference in the performance of the piglets. The melatonin concentrations in the saliva of piglets at 10 and 20 days of age in the three treatments showed different diurnal rhythms, but there was no significant difference in the levels of melatonin in TL piglets between night and day. Differences in salivary cortisol levels only appeared between the CE and RL groups at 20 days of age. Based on the present results, the illuminance and spectrum of the transparent heat lamps were sufficient to stimulate sow activity and inhibit melatonin levels in piglets. However, the stimulating effect on suckling was not sufficient to significantly improve the performance of piglets. Exposure to red heat lamps, rather than ceramic lamps, resulted in the strongest circadian rhythm of salivary melatonin in piglets.     

Multiplex gene precise editing and large DNA fragment deletion by the CRISPR-Cas9-TRAMA system in edible mushroom Cordyceps militaris

The medicinal mushroom Cordyceps militaris contains abundant valuable bioactive ingredients that have attracted a great deal of attention in the pharmaceutical and cosmetic industries. However, the development of this valuable mushroom faces the obstacle of lacking powerful genomic engineering tools. Here, by excavating the endogenous tRNA-processed element, introducing the extrachromosomal plasmid and alongside with homologous template, we develop a marker-free CRISPR-Cas9-TRAMA genomic editing system to achieve the multiplex gene precise editing and large synthetic cluster deletion in C. militaris. We further operated editing in the synthetases of cordycepin and ergothioneine to demonstrate the application of Cas9-TRAMA system in protein modification, promoter strength evaluation and 10 kb metabolic synthetic cluster deletion. The Cas9-TRAMA system provides a scalable method for excavating the valuable metabolic resource of medicinal mushrooms and constructing a mystical cellular pathway to elucidate the complex cell behaviours of the edible mushroom.     

Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron

Standard plant DNA barcodes based on 2–3 plastid regions, and nrDNA ITS show variable levels of resolution, and fail to discriminate among species in many plant groups. Genome skimming to recover complete plastid genome sequences and nrDNA arrays has been proposed as a solution to address these resolution limitations. However, few studies have empirically tested what gains are achieved in practice. Of particular interest is whether adding substantially more plastid and nrDNA characters will lead to an increase in discriminatory power, or whether the resolution limitations of standard plant barcodes are fundamentally due to plastid genomes and nrDNA not tracking species boundaries. To address this, we used genome skimming to recover near-complete plastid genomes and nuclear ribosomal DNA from Rhododendron species and compared discrimination success with standard plant barcodes. We sampled 218 individuals representing 145 species of this species-rich and taxonomically difficult genus, focusing on the global biodiversity hotspots of the Himalaya-Hengduan Mountains. Only 33% of species were distinguished using ITS+matK+rbcL+trnH-psbA. In contrast, 55% of species were distinguished using plastid genome and nrDNA sequences. The vast majority of this increase is due to the additional plastid characters. Thus, despite previous studies showing an asymptote in discrimination success beyond 3–4 plastid regions, these results show that a demonstrable increase in discriminatory power is possible with extensive plastid genome data. However, despite these gains, many species remain unresolved, and these results also reinforce the need to access multiple unlinked nuclear loci to obtain transformative gains in species discrimination in plants.     

Probiotic Therapy (BIO-THREE) Mitigates Intestinal Microbial Imbalance and Intestinal Damage Caused by Oxaliplatin

Probiotics and Antimicrobial Proteins - Gastrointestinal mucositis associated with the use of chemotherapeutic drugs can seriously affect the quality of life of patients. In this study, a probiotic...     

Erythrocyte immune system: beyond the gas transporter

Accumulating research has revealed that erythrocytes play unique roles in the innate immune system. Once thought of as immunologically inert cells, erythrocytes are functional cells that exert diverse immunological effects. Although mature mammal erythrocytes lack internal organelles, they express various receptors, which provide an extraordinary ability for erythrocytes to clear or sequester circulating molecules that affect immune functions. In this review, we elucidate some crucial immunological molecules associated with erythrocytes, such as CR1, CD47, TLR9, and cytokines. CR1 acts as a bridge in clearing off immune complexes and an entrance gate for some pathogens. CD47, once bound to SIRPα, generates an inhibitory signal in macrophage phagocytosis. Reciprocally, erythrocyte CD47 undergoes a conformational change during oxidative stress-induced cellular senescence, subsequently activating phagocytic signals through binding to TSP-1. TLR9 recognizes unmethylated CpG-DNA present in viruses and bacteria. Erythrocyte TLR9 also binds to and eliminates mitochondrial DNA. Erythrocytes can recruit chemokines and modulate plasma chemokine levels through the Duffy antigen receptor for chemokines (DARC). Moreover, erythrocytes may exert immune functions by releasing danger-associated molecular patterns (DAMPs), i.e., heme, IL-33, ATP, and Hsp70. Heme bound with toll-like receptor 4 (TLR4) has the potential to trigger an inflammatory response. Similarly, IL-33, ATP, and Hsp70 from damaged erythrocytes may be involved in the innate immune response via diverse signaling mechanisms. This review provides novel insight into the immunological functions of erythrocytes, which play an irreplaceable role in innate immune responses. We argue that erythrocyte-involved immune function is a widespread area warranting intensive investigation.     

Activity based fingerprinting of proteases using FRET peptides

We have successfully developed a protease assay using fluorescence resonance energy transfer based peptide libraries, which allows not only general detection of enzymatic activities, but more importantly substrate fingerprinting of proteases from different classes. The method allows the generation of substrate fingerprints of a protease from both the nonprime and prime sites. Therefore, it is well suited for profiling of major metalloproteases such as thermolysin and MMPs. We envisage that this method will provide a useful tool in the emerging field of Catalomics for high-throughput studies of proteases.     

Spectroscopic and molecular modeling studies of the interaction between cytidine and human serum albumin and its analytical application

In this study, the interaction between cytidine and human serum albumin (HSA) was investigated for the first time by fluorescence spectroscopy in combination with UV absorption spectrum and molecular modeling under simulative physiological conditions. Experimental results indicated that cytidine had a strong ability to quench the intrinsic fluorescence of human serum albumin. The binding constants (K) at different temperatures, thermodynamic parameter enthalpy changes (DeltaH) and entropy changes (DeltaS) of HSA-cytidine had been calculated according to the relevant fluorescence data, which indicated that the hydrophobic and electrostatic interactions played a major role, which was in agreement with the results of molecular modeling study. In addition, the effects of other ions on the binding constants were also studied. Furthermore, synchronous fluorescence technology was successfully applied to the determination of human serum albumin added into the cytidine solution.     

Merozoite surface protein 2 of Plasmodium falciparum: expression, structure, dynamics, and fibril formation of the conserved N-terminal domain

Merozoite surface protein 2 (MSP2) is a GPI-anchored protein on the surface of the merozoite stage of the malaria parasite Plasmodium falciparum. It is largely disordered in solution, but has a propensity to form amyloid-like fibrils under physiological conditions. The N-terminal conserved region (MSP2(1-25)) is part of the protease-resistant core of these fibrils. To investigate the structure and dynamics of this region, its ability to form fibrils, and the role of individual residues in these properties, we have developed a bacterial expression system that yields > or =10 mg of unlabeled or (15)N-labeled peptide per litre of culture. Two recombinant versions of MSP2(1-25), wild-type and a Y7A/Y16A mutant, have been produced. Detailed conformational analysis of the wild-type peptide and backbone (15)N relaxation data indicated that it contains beta-turn and nascent helical structures in the central and C-terminal regions. Residues 6-21 represent the most ordered region of the structure, although there is some flexibility around residues 8 and 9. The 10-residue sequence (MSP2(7-16)) (with two Tyr residues) was predicted to have a higher propensity for beta-aggregation than the 8-mer sequence (MSP2(8-15)), but there was no significant difference in conformation between MSP2(1-25) and [Y7A,Y16A]MSP2(1-25) and the rate of fibril formation was only slightly slower in the mutant. The peptide expression system described here will facilitate further mutational analyses to define the roles of individual residues in transient structural elements and fibril formation, and thus contribute to the further development of MSP2 as a malaria vaccine candidate.     

lpp deletion as a permeabilization method

Our earlier studies with outer membrane permeability in E. coli showed that an insertion mutation in lpp gene (encoding Braun's lipoprotein) drastically changed the outer membrane permeability, resulting in significant acceleration of whole-cell catalyzed reactions. In order to gain a mechanistic understanding of the nature of permeability change, the lpp region was sequenced. The results revealed that Lpp was not expressed in the insertion mutant, suggesting that the absence, rather than the alteration, of Lpp is responsible for the observed permeability change. This surprising result prompts us to investigate the possibility of establishing lpp deletion as a general permeabilization method. Two lpp deletion mutants were generated from strains with different genetic background and the effect of lpp deletion on cell physiology was investigated. While lpp deletion had no significant effect on cell growth, carbon metabolism, and fatty acid compositions, it enhanced permeability of various small molecules, consistent with the results with the insertion mutant. This phenotype is useful in a wide range of biotechnological applications. We illustrate here the use of the mutant with organophosphate hydrolysis and L-carnitine synthesis, where permeability is known to be a limiting factor. Both processes were significantly improved with the mutant because of enhanced permeability through the outer membrane. Therefore, this study has established an easy yet generally applicable method for permeabilizing E. coli cells without significant adverse effects. Further, as lpp homolog is known to exist in gram-negative bacteria, we expect that this method will be applicable to other gram-negative bacteria.