Interplay Between Intracellular Transport Dynamics and Liquid-Liquid Phase Separation.

Liquid-liquid phase separation (LLPS) is a ubiquitous process in which proteins, RNA, and biomolecules assemble into membrane-less compartments, playing important roles in many biological functions and diseases. The current knowledge on the biophysical and biochemical principles of LLPS is largely from in vitro studies; however, the physiological environment in living cells is complex and not at equilibrium. The characteristics of intracellular dynamics and their roles in physiological LLPS remain to be resolved. Here, by using single-particle tracking of quantum dots and dynamic monitoring of the formation of stress granules (SGs) in single cells, the spatiotemporal dynamics of intracellular transport in cells undergoing LLPS are quantified. It is shown that intracellular diffusion and active transport are both reduced. Furthermore, the formation of SG droplets contributes to increased spatial heterogeneity within the cell. More importantly, the study demonstrated that the LLPS of SGs can be regulated by intracellular dynamics in two stages: the reduced intracellular diffusion promotes SG assembly and the microtubule-associated transport facilitates SG coalescences. The work on intracellular dynamics not only improves the understanding of the mechanism of physiology phase separations occurring in nonequilibrium environments but also reveals an interplay between intracellular dynamics and LLPS.

Intestinal schistosomiasis masquerading as intestinal polyps.

BACKGROUND: Schistosomiasis is very common in the southern part of the Yangtze River Basin in China. It is mainly manifested as appendicitis, ulcers, hematomas, and thickening of the intestinal tract. Schistosomiasis of the appendix is rare, mainly manifested as appendicitis, which is easy to be misdiagnosed. CASE PRESENTATION: Here we report a rare case of a Chinese female whose intestinal mass manifested as intestinal polyps and was eventually diagnosed pathologically as schistosomiasis infection (appendix schistosomiasis). So far, there are rare relevant cases reported. CONCLUSIONS: Intestinal schistosomiasis is easily misdiagnosed, and appendix schistosomiasis is rare. The final diagnosis requires pathology, especially surgical pathology.

Intracellular transport dynamics revealed by single-particle tracking.

Intracellular transport is the basis for the transfer of matter, energy, and information in cells and is critical to many cellular functions. Within the nonequilibrium environment of living cells, the transport behaviours are far from the traditional motion in liquid but are more complex and active. With the advantage of high spatial and temporal resolution, the single-particle tracking (SPT) method is widely utilized and has achieved great advances in revealing intracellular transport dynamics. This review describes intracellular transport from a physical perspective and classifies it into two modes: diffusive motion and directed motion. The biological functions and physical mechanisms for these two transport modes are introduced. Next, we review the principle of SPT and its advances in two aspects of intracellular transport. Finally, we discuss the prospect of near infrared SPT in exploring the in vivo intracellular transport dynamics.

miRNA-186 Improves Sepsis Induced Renal Injury Via PTEN/PI3K/AKT/P53 Pathway.

AIM: The aim of this study is to explain the effects of miRNA-186 in renal injury induced by sepsis. METHODS: The Wistar rats were divided into 3 groups: the Sham group, Sepsis model group and the miRNA-186 group based on the model group; there were 9 rats in every group. The rat sepsis model was reproduced by cecal ligation and puncture (CLP). The rats of the miRNA-186 group were injected miRNA-186 from caudal vein. The rats of the difference group were killed after operation 24 h. The kidneys of the difference groups were taken for histopathological and cell apoptosis analysis by H&E and TUNEL assay. The relative protein expressions were measured by WB assay. miRNA-186 target to Phosphatase and tensin homologous protein (PTEN). RESULTS: Compared with the Sham group, the kidney histopathological and cell apoptosis rates of the model group were significantly damaged (P<0.05, respectively), however, the kidney histopathological and cell apoptosis rate of miRNA-186 group were significantly improved compared with the model group (P<0.05, respectively). The relative protein expressions were significantly different among 3 groups (P<0.05, respectively). The PTEN was the target of the miRNA-186. CONCLUSION: miRNA-186 over-expression has effects that improve renal injury induced by sepsis via PTEN pathway.

A comprehensive evaluation of a typical plant telomeric G-quadruplex (G4) DNA reveals the dynamics of G4 formation, rearrangement, and unfolding.

Telomeres are specific nucleoprotein structures that are located at the ends of linear eukaryotic chromosomes and play crucial roles in genomic stability. Telomere DNA consists of simple repeats of a short G-rich sequence: TTAGGG in mammals and TTTAGGG in most plants. In recent years, the mammalian telomeric G-rich repeats have been shown to form G-quadruplex (G4) structures, which are crucial for modulating telomere functions. Surprisingly, even though plant telomeres are essential for plant growth, development, and environmental adaptions, only few reports exist on plant telomeric G4 DNA (pTG4). Here, using bulk and single-molecule assays, including CD spectroscopy, and single-molecule FRET approaches, we comprehensively characterized the structure and dynamics of a typical plant telomeric sequence, d[GGG(TTTAGGG)3]. We found that this sequence can fold into mixed G4s in potassium, including parallel and antiparallel structures. We also directly detected intermediate dynamic transitions, including G-hairpin, parallel G-triplex, and antiparallel G-triplex structures. Moreover, we observed that pTG4 is unfolded by the AtRecQ2 helicase but not by AtRecQ3. The results of our work shed light on our understanding about the existence, topological structures, stability, intermediates, unwinding, and functions of pTG4.

Expression and epitope identification of myosin light chain isoform 1, an allergen in Procambarus clarkii.

Myosin light chain isoform 1 (MLC1) is reported to be a novel allergen in crayfish (Procambarus clarkii). However, little information is available about its allergic epitopes. In this study, recombinant crayfish MLC1 (rMLC1) was expressed and confirmed by mass spectrometry. Circular dichroic analysis and serological test were performed for the measuring of structural and immunological properties of rMLC1. Specific-protein-A-enriched IgG raised in rabbits against purified rMLC1 was used to screen a phage display random peptide library. Nine MLC1 mimotope clones were identified among 16 random clones after biopanning. Five conformational epitopes were identified with the program LocaPep, and mapped into 3 epitope regions at the antibody-binding interface of MLC1. MLC1 of crayfish showed high primary and secondary structure identity to MLC of other allergenic species, its epitopes were located in the structure conserved regions, and its cross-reactivity among related species was indicated by immunological assays.

Studying the Potassium-Induced G-Quadruplex DNA Folding Process Using Microscale Thermophoresis.

Guanine (G) quadruplexes (G4s) can be formed by G-rich sequences when stabilized by the binding of cations (typically K+ or Na+) and play an essential role in replication, recombination, transcription, and telomere maintenance. Understanding of the G4 folding process is crucial for determining their cellular functions. However, G4-K+ interactions and folding pathways are still not well understood. By using human telomeric G4 (hTG4) as an example, two binding states corresponding to two K+ cations binding to hTG4 were distinguished clearly and fitted precisely. The basic binding parameters during G4-K+ interactions were measured and calculated by taking advantage of microscale thermophoresis (MST), which monitors the changes in charge and size at the same time. The G-hairpin and G-triplex have been suggested as intermediates during G4 folding and unfolding. We further analyzed the equilibrium dissociation constants of 10 possible folding intermediates using MST; thus, the energetically favorable folding/unfolding pathways were proposed. The results might not only shed new light on G4-K+ interactions and G4 folding pathways but also provide an example for experimentally studying DNA-ion interactions.

Pleistocene climate change and phylogeographic structure of the Gymnocarpos przewalskii (Caryophyllaceae) in the northwest China: Evidence from plastid DNA, ITS sequences, and Microsatellite.

Northwestern China has a wealth of endemic species, which has been hypothesized to be affected by the complex paleoclimatic and paleogeographic history during Quaternary. In this paper, we used Gymnocarpos przewalskii as a model to address the evolutionary history and current population genetic structure of species in northwestern China. We employed two chloroplast DNA fragments (rps16 and psbB-psbI), one nuclear DNA fragment (ITS), and simple sequence repeat (SSRs) to investigate the spatial genetic pattern of G. przewalskii. High genetic diversity (cpDNA: h S = 0.330, h T = 0.866; ITS: h S = 0.458, h T = 0.872) was identified in almost all populations, and most of the population have private haplotypes. Moreover, multimodal mismatch distributions were observed and estimates of Tajima's D and Fu's FS tests did not identify significantly departures from neutrality, indicating that recent expansion of G. przewalskii was rejected. Thus, we inferred that G. przewalskii survived generally in northwestern China during the Pleistocene. All data together support the genotypes of G. przewalskii into three groups, consistent with their respective geographical distributions in the western regions-Tarim Basin, the central regions-Hami Basin and Hexi Corridor, and the eastern regions-Alxa Desert and Wulate Prairie. Divergence among most lineages of G. przewalskii occurred in the Pleistocene, and the range of potential distributions is associated with glacial cycles. We concluded that climate oscillation during Pleistocene significantly affected the distribution of the species.

Reducing Allergenicity to Arginine Kinase from Mud Crab Using Site-Directed Mutagenesis and Peptide Aptamers.

The mud crab ( Scylla paramamosain) is widely consumed but can cause a severe food allergic reaction. To reduce allergenicity to arginine kinase (AK), site-directed mutagenesis was used to destroy disulfide bonds or mutate critical amino acids of conformational epitopes. Three hypoallergenic mutant AKs (mAK1, mAK2, and mAK3) were generated, with the immunoreactivity decreasing by 54.2, 40.1, and 71.4%, respectively. In comparison to recombinant AK (rAK), the structure of mAKs was clearly changed. Additionally, antisense peptides were designed on the basis of linear epitopes and pepsin-cutting sites of AK. Five peptide aptamers were screened by molecular docking and then analyzed by the immunoglobulin E inhibition enzyme-linked immunosorbent assay and human Laboratory of Allergic Diseases 2 mast cell degranulation assay. The peptide aptamers could significantly inhibit allergenicity of rAK and mAKs, and the inhibitory effect of peptide aptamer 3 was slightly better than the others. These results provide synergistic methods to reduce allergenicity to AK, which could be applied to other shellfish allergens.

A comprehensive analysis of the allergenicity and IgE epitopes of myosinogen allergens in Scylla paramamosain.

BACKGROUND: Scylla paramamosain is one of the most common and serious food allergens in Asia. Therefore, research on its prevalence, accurate diagnosis, and IgE-binding pattern of the allergens is crucial. OBJECTIVE: To identify the IgE epitopes of the myosinogen allergens in S. paramamosain using phage peptide library. METHODS: The prevalence of allergy to crabs (AC) and of sensitization was analysed using a questionnaire and a serological assay. BAT was performed by flow cytometry, and its diagnostic performance was evaluated in relation to allergens purified from crab myosinogen. IgE-binding epitopes were identified by phage display using the IgE from patients with AC. Sequence- and structure-based bioinformatics analyses were performed to identify allergenic epitopes. RESULTS: Crab was the most common cause of food allergies in this study. Subjects with AC (n = 30) with clear clinical symptoms were identified by immunoblotting and BAT. All of the myosinogen allergens triggered basophil activation; surface expression of CD63 and CD203c was higher in patients allergic to AK and FLN c than in patients allergic to SCP and TIM. In addition to six conformational epitopes of SCP, six linear epitopes and eight conformational epitopes of AK were identified. Five linear epitopes and three conformational epitopes of TIM, nine linear and ten conformational epitopes of FLN c were also identified, and the sequence VH(I/T) L was appeared in epitopes of both TIM and FLN c. The number of epitopes showed consistency with the value of BAT. CONCLUSIONS AND CLINICAL RELEVANCE: BAT can be used for accurate diagnosis of AC. Identification of particular allergenic motifs could be a valuable tool for prevention, diagnosis, and treatment of food allergies.

Analysis of the Allergenic Epitopes of Tropomyosin from Mud Crab Using Phage Display and Site-Directed Mutagenesis.

Mud crab ( Scylla serrata), which is widely consumed, can cause severe allergic symptoms. Eight linear epitopes and seven conformational epitopes of tropomyosin (TM) from S. serrata were identified using phage display. The conformational epitopes were formed based on the coiled-coil structure of TM. Most of the epitopes were located in the regions where primary structures were conserved among crustacean TM. Twelve synthetic peptides were designed according to the epitopes and trypsin-cutting sites of TM, among them, three synthetic peptides (including one linear epitope and two conformational epitopes) were recognized by all of the patient sera using inhibitory dot blotting. A triple-variant (R90A-E164A-Y267A) was constructed based on the critical amino acids of the TM epitope. The IgE-binding activity of the triple-variant was significantly reduced compared with that of native TM. The results of phage display and site-directed mutagenesis offered new information regarding conformational epitopes of TM.

Insight into Central Asian flora from the Cenozoic Tianshan montane origin and radiation of Lagochilus (Lamiaceae).

The Tianshan Mountains play a significant role in the Central Asian flora and vegetation. Lagochilus has a distribution concentration in Tianshan Mountains and Central Asia. To investigate generic spatiotemporal evolution, we sampled most Lagochilus species and sequenced six cpDNA locations (rps16, psbA-trnH, matK, trnL-trnF, psbB-psbH, psbK-psbI). We employed BEAST Bayesian inference for dating, and S-DIVA, DEC, and BBM for ancestral area/biome reconstruction. Our results clearly show that the Tianshan Mountains, especially the western Ili-Kirghizia Tianshan, as well as Sunggar and Kaschgar, was the ancestral area. Ancestral biome was mainly in the montane steppe zone of valley and slope at altitudes of 1700-2700 m, and the montane desert zone of foothill and front-hill at 1000-1700 m. Here two sections Inermes and Lagochilus of the genus displayed "uphill" and "downhill" speciation process during middle and later Miocene. The origin and diversification of the genus were explained as coupled with the rapid uplift of the Tianshan Mountains starting in late Oligocene and early Miocene ca. 23.66~19.33 Ma, as well as with uplift of the Qinghai-Tibetan Plateau (QTP) and Central Asian aridification.

Triosephosphate Isomerase and Filamin C Share Common Epitopes as Novel Allergens of Procambarus clarkii.

Triosephosphate isomerase (TIM) is a key enzyme in glycolysis and has been identified as an allergen in saltwater products. In this study, TIM with a molecular mass of 28 kDa was purified from the freshwater crayfish (Procambarus clarkii) muscle. A 90-kDa protein that showed IgG/IgE cross-reactivity with TIM was purified and identified as filamin C (FLN c), which is an actin-binding protein. TIM showed similar thermal and pH stability with better digestion resistance compared with FLN c. The result of the surface plasmon resonance (SPR) experiment demonstrated the infinity of anti-TIM polyclonal antibody (pAb) to both TIM and FLN c. Five linear and 3 conformational epitopes of TIM, as well as 9 linear and 10 conformational epitopes of FLN c, were mapped by phage display. Epitopes of TIM and FLN c demonstrated the sharing of certain residues; the occurrence of common epitopes in the two allergens accounts for their cross-reactivity.

Spatial Patterns of Species Diversity and Phylogenetic Structure of Plant Communities in the Tianshan Mountains, Arid Central Asia.

The Tianshan Mountains, located in arid Central Asia, have a humid climate and are biodiversity hotspots. Here, we aimed to clarify whether the pattern of species diversity and the phylogenetic structure of plant communities is affected by environmental variables and glacial refugia. In this study, plant community assemblies of 17 research sites with a total of 35 sample plots were investigated at the grassland/woodland boundaries on the Tianshan Mountains. Community phylogeny of these plant communities was constructed based on two plant DNA barcode regions. The indices of phylogenetic diversity and phylogenetic community structure were calculated for these sample plots. We first estimated the correlation coefficients between species richness (SR) and environmental variables as well as the presence of glacial refugia. We then mapped the significant values of indices of community phylogeny (PD, RPD, NRI, and NTI) to investigate the correlation between community phylogeny and environmental structure or macrozones in the study area. The results showed that a significantly higher value of SR was obtained for the refugial groups than for the colonizing groups (P < 0.05); presence of refugia and environmental variables were highly correlated to the pattern of variation in SR. Indices of community phylogeny were not significantly different between refugial and colonizing regions. Comparison with the humid western part showed that plant communities in the arid eastern part of the Tianshan Mountains tended to display more significant phylogenetic overdispersion. The variation tendency of the PhyloSor index showed that the increase in macro-geographical and environmental distance did not influence obvious phylogenetic dissimilarities between different sample plots. In conclusion, glacial refugia and environmental factors profoundly influenced the pattern of SR, but community phylogenetic structure was not affected by glacial refugia among different plant communities on the Tianshan Mountains. This pattern of community phylogenetic structure could have resulted from shared ancestry and species pool among these sample plots.

Himalayan uplift shaped biomes in Miocene temperate Asia: evidence from leguminous Caragana.

Caragana, with distinctive variation in leaf and rachis characters, exhibits three centers of geographic distribution, i.e., Central Asia, the Qinghai-Tibetan Plateau (QTP), and East Asia, corresponding to distinct biomes. Because Caragana species are often ecologically dominant components of the vegetation in these regions, it is regarded as a key taxon for the study of floristic evolution in the dry regions of temperate Asia. Based on an expanded data set of taxa and gene regions from those previously generated, we employed molecular clock and biogeographical analyses to infer the evolutionary history of Caragana and link it to floristic patterns, paleovegetation, and paleoclimate. Results indicate that Caragana is of arid origin from the Junggar steppe. Diversification of crown group Caragana, dated to the early Miocene ca. 18 Ma and onwards, can be linked to the Himalayan Motion stage of QTP uplift. Diversification of the major clades in the genus corresponding to taxonomic sections and morphological variation is inferred to have been driven by the uplift, as well as Asian interior aridification and East Asian monsoon formation, in the middle to late Miocene ca. 12~6 Ma. These findings demonstrate a synchronous evolution among floristics, vegetation and climate change in arid Central Asia, cold arid alpine QTP, and mesophytic East Asia.

Phylogeographic History of Atraphaxis Plants in Arid Northern China and the Origin of A. bracteata in the Loess Plateau.

In China, species of Atraphaxis (Polygonaceae) primarily inhabit arid zones across temperate steppe and desert regions. The complex geologic history (e.g., expansion of deserts) and extreme climate shifts of the region appear to have played an important role in shaping the phylogeography of Atraphaxis. The present study focuses on species-level phylogeographic patterns of Atraphaxis in China, with the goal of determining the impact of past environmental changes, in northern China, on the evolutionary history of the genus. Five hundred and sixty-four individuals distributed among 71 populations of 11 species of Atraphaxis from across the geographic range of the genus were studied using sequence data from two plastid spacers, psbK-psbI and psbB-psbH. The results demonstrate that most chloroplast haplotypes are species-specific, except for some present among widespread species. The phylogeny of Atraphaxis was well structured, and molecular dating analyses suggest that the main divergence events occurred during the late Pliocene and Pleistocene (5.73-0.03 million years ago). The statistical dispersal-vicariance analysis (S-DIVA) results provide evidence that phylogeographic patterns for the genus were characterized by both vicariance events and regional dispersal. The presented data suggest that the rapid expansion of deserts and climatic changes in northern China during the late Pliocene and Pleistocene have driven the diversification and spread of Atraphaxis in the region. The expansion of the Tengger Desert provided appropriate conditions for the origin of A. bracteata. Additionally, a contact zone in the north of the Hexi Corridor was identified as having played a significant role as a migratory route for species in adjacent areas.

Evolutionary History of a Desert Shrub Ephedra przewalskii (Ephedraceae): Allopatric Divergence and Range Shifts in Northwestern China.

Based on two chloroplast DNA sequences, psbA-trnH and trnT-trnF, phylogeographical patterns of a desert shrub, Ephedra przewalskii, were examined across most of its geographic range in northwestern China. A total of sixteen haplotypes were detected. There was a common haplotype in each basin, that was haplotype A in Tarim Basin, haplotype G in Junggar Basin, and haplotype M in Qaidam Basin. Genetic variance mainly occurred among populations, geographic regions, and eleven geographic groups subdivided by SAMOVA analysis. E. przewalskii likely had a smaller and more fragmented geographic range during the Last Glacial Maximum, which was determined based on ecological niche modelling. Three groups of E. przewalskii populations were detected to have experience range expansion, and this was based on significant values of Fu's FS, Tajima's D, and unimodel mismatch distributions. The cold and dry climate during the glacial period of the Quaternary is postulated to have been a driver for significant genetic isolation and divergence among populations or groups in E. przewalskii, whereas the warmer and wetter climate during the interglacial period is speculated to have provided favourable conditions for range expansion of the species.

Phylogeographic Structure of a Tethyan Relict Capparis spinosa (Capparaceae) Traces Pleistocene Geologic and Climatic Changes in the Western Himalayas, Tianshan Mountains, and Adjacent Desert Regions.

Complex geological movements more or less affected or changed floristic structures, while the alternation of glacials and interglacials is presumed to have further shaped the present discontinuous genetic pattern of temperate plants. Here we consider Capparis spinosa, a xeromorphic Tethyan relict, to discuss its divergence pattern and explore how it responded in a stepwise fashion to Pleistocene geologic and climatic changes. 267 individuals from 31 populations were sampled and 24 haplotypes were identified, based on three cpDNA fragments (trnL-trnF, rps12-rpl20, and ndhF). SAMOVA clustered the 31 populations into 5 major clades. AMOVA suggests that gene flow between them might be restricted by vicariance. Molecular clock dating indicates that intraspecific divergence began in early Pleistocene, consistent with a time of intense uplift of the Himalaya and Tianshan Mountains, and intensified in mid-Pleistocene. Species distribution modeling suggests range reduction in the high mountains during the Last Glacial Maximum (LGM) as a result of cold climates when glacier advanced, while gorges at midelevations in Tianshan appear to have served as refugia. Populations of low-altitude desert regions, on the other hand, probably experienced only marginal impacts from glaciation, according to the high levels of genetic diversity.

The relationship of spectral sensitivity with growth and reproductive response in avian breeders (Gallus gallus).

A previous study demonstrated that birds that are exposed to light at night develop advanced reproductive systems. However, spectrum might also affect the photoperiodic response of birds. The present study was aimed to investigate the effects of spectral composition on the growth and reproductive physiology of female breeders, using pure light-emitting diode spectra. A total of 1,000 newly hatched female avian breeders (Gallus gallus) were equally allocated to white-, red-, yellow-, green- and blue-light treated groups. We found that blue-light treated birds had a greater and faster weight gain than did red- and yellow-light treated birds (P = 0.02 and 0.05). The red light expedited the sexual maturation of the chicks, whose age at sexual maturity was 7 and 14 days earlier than that of the green- and blue-light treated birds, respectively. The accumulative egg production of the red-light treated birds was 9 and 8 eggs more than that of the blue- and green-light treated birds. The peak lay rate of the red-light treated groups was significantly greater than the blue-light treated birds (P = 0.028). In conclusion, exposure to short-wavelength light appears to promote growth of female breeder birds, whereas exposure to long-wavelength light appears to accelerate reproductive performance.

Young dispersal of xerophil Nitraria lineages in intercontinental disjunctions of the Old World.

Many cases of intercontinental disjunct distributions of seed plants have been investigated, however few have concerned the continents of Eurasia (mainly Central Asia), Africa, and Australia, especially the xerophytic lineages are lacking. Nitraria (Nitrariaceae) is just one of these xerophytic lineages. Previous Nitraria studies have hypothesized either Africa as the ancient center, with dispersals to Australia and Eurasia, or alternatively Central Asia, due to a concentration of endemism and diversity there. Our findings show eastern Central Asia, i.e. the eastern Tethys, to be the correct place of origin. Dispersal westward to Africa occurred during the late Oligocene to Pliocene, whereas dispersal to Australia from western Central Asia was young since Pliocene 2.61 Ma. Two related tetraploids are indicated to have diversified in eastern Central Asia at approximately 5.89 Ma, while the Australian tetraploid N. billardieri, is an independently derived, recent dispersal from western Central Asia.