[X-linked neutropenia caused by gain-of-function mutation in WAS gene: two cases report and literature review]

Objective: To investigate the clinical and genotypic manifestations of X-linked neutropenia caused by gain-of-function mutation in WAS gene. Methods: The clinical history of two patients with X-linked neutropenia caused by gain-of-function mutation in WAS gene in Shenzhen Children's Hospital were analyzed."X-linked neutropenia" and "WAS mutation" were used as key words to search related literatures published from January 2000 to December 2018 in CNKI,Wanfang, and Pubmed databases. Results: The first case was male,1 year old, admitted for 1 year of neutropenia combined with 5 days of cough and 3 days of fever. Persistent neutropenia (0.1×10(9)-0.3×10(9)/L) was reported before admission and during hospitalization (0.4×10(9)-0.5×10(9)/L). The patient was treated with Ciprofloxacin, cefoperazone sulbactam and Vancomycin,and relieved from fever after 4 weeks of hospitalization,yet the neutropenia (0.1×10(9)-0.6×10(9)/L) continued after discharge. Variant in WAS gene (c.T869C (p.I290T) ) was identified, and the percentage of WAS protein on lymphocyte was 97.7%. The second case was male, 42 days old,admitted for fever and neutropenia (0.5×10(9)/L). Similarly,he relieved from fever after 4 weeks of treatment with amoxicillin sulbactam,vancomysin,meropenem,rifampin and isoniacid,yet was discharged with continued neutropenia. Variant in WAS gene (c.T881C (p.I294T)) was identified and the percentage of WAS protein on lymphocyte was 92%. Published literature reported four variants,including I290T, L270P, S272P and I294T, as the pathogenic mutation of X-linked neutropenia in 18 patients from five families. Neutropenia (0.1×10(9)-1.0×10(9)/L) were reported in 15 patients,while normal neutrophil number was found in the rest. Recurrent infection,mainly pneumonia and otitis media,was the most common clinical manifestation. Conclusions: Neutropenia is the prominent presentation in the patients with X-linked neutropenia caused by gain-of-function mutation in WAS gene, but it unnecessarily correlates with the clinical severity in terms of infection. Gene sequencing should be considered for the male patients with persistent neutropenia.

Temporal variation and photochemical efficiency of species in Symbiodinaceae associated with coral Leptoria phrygia (Scleractinia; Merulinidae) exposed to contrasting temperature regimes

The Symbiodinaceae are paradoxical in that they play a fundamental role in the success of scleractinian corals, but also in their dismissal when under stress. In the past decades, the discovery of the endosymbiont's genetic and functional diversity has led people to hope that some coral species can survive bleaching events by associating with a stress-resistant symbiont that can become dominant when seawater temperatures increase. The variety of individual responses encouraged us to scrutinize each species individually to gauge its resilience to future changes. Here, we analyse the temporal variation in the Symbiodinaceae community associated with Leptoria phrygia, a common scleractinian coral from the Indo-Pacific. Coral colonies were sampled from two distant reef sites located in southern Taiwan that differ in temperature regimes, exemplifying a 'variable site' (VS) and a 'steady site' (SS). We investigated changes in the relative abundance of the dominant symbiont and its physiology every 3-4 months from 2016-2017. At VS, 11 of the 12 colonies were dominated by the stress-resistant Durusdinium spp. (>90% dominance) and only one colony exhibited co-dominance between Durusdinium spp. and Cladocopium spp. Every colony displayed high photochemical efficiency across all sampling periods, while showing temporal differences in symbiont density and chlorophyll a concentration. At SS, seven colonies out of 13 were dominated by Cladocopium spp., five presented co-dominance between Durusdinium spp./Cladocopium spp. and only one was dominated by Durusdinium spp. Colonies showed temporal differences in photochemical efficiency and chlorophyll a concentration during the study period. Our results suggest that VS colonies responded physiologically better to high temperature variability by associating with Durusdinium spp., while in SS there is still inter-colonial variability, a feature that might be advantageous for coping with different environmental changes.

[Effect of miR-21 on the expression of interleukin-10 in B cell of patients with Henoch-Schonlein purpura]

Objective: To investigate the effect of microRNAs (miR)-21 on the expression of interleukin (IL)-10 in B cell of patients with Henoch-Schonlein purpura (HSP). Methods: From March 2016 to January 2017, twenty-four children with HSP hospitalized in rheumatology and immunology department of Shenzhen Children's Hospital were enrolled into the study, including 12 males and 12 females. Patients were divided into purpura nephritis group (HSPN, 14 cases) and non-nephritis group (NHSPN, 10 cases). The age-matched 34 healthy children were included as the control group for prospective cohort study. The expression levels of IL-10 in peripheral blood B cells (CD19(+)), transitional B cells (CD19(+) CD24(hi)CD38(hi)) and naïve B cells (CD19(+)CD24(int)CD38(int)) from patients with HSP and healthy children were detected by flow cytometry (FCM). Expression of microRNAs related to IL-10 in B cells were quantitated by real-time PCR, including miR-21-5p, miR-106a-5p, miR-98-3p, miR-142-3p, miR-142-5p, miR-98-5p, miR-155-5p and miR-let7b-5p. Agomir negative control-FAM and agomir-21-5p-FAM were transfected into B cells from patients with HSP. The uptake of miRNA by B cells was observed by laser scanning confocal microscope and FCM, and the expression of IL-10 was detected by FCM after transfection. For quantitative data of normal distribution, t test was used for two samples comparison and multiple comparisons among three groups were conducted by ANOVA. Spearman test was used for correlation analysis. Results: (1) The CD19(+) B cells and its two populations at different differentiation stages all could express IL-10. The expression levels of IL-10 in three B cell populations in patients were significantly lower than those in healthy controls (1.4±0.2 vs. 2.4±0.3, t=3.501, P<0.01; 1.2±0.2 vs. 2.2±0.3, t=2.688, P<0.05; 1.6±0.3 vs. 2.7±0.4, t=2.498, P<0.05). Compared with healthy control and NHSPN groups, the expression of IL-10 in CD19(+) B cells from patients within HSPN group was the lowest, and the difference was statistically significant (1.1±0.2 vs. 2.4±0.3, 1.8±0.3, t=4.006, 2.362, P<0.001, P<0.05). (2) The expression of miR-21-5p in B cell in patients with HSPN was lower than that in healthy control group (1.2±0.9 vs. 3.5±2.8, t=2.962, P<0.01). There was no significant change in the other microRNAs. (3) The expression of IL-10 was positively correlated with the expression of miR-21-5p in the B cells of patients with HSP (r=0.778, P<0.001). (4) The expression of IL-10 in B cells of miR-21-5p group was significantly higher than that in negative control group (2.7±0.2 vs. 1.6±0.3, t=3.091, P<0.05). Conclusion: The insufficient expression of miR-21-5p in peripheral blood B cells of patients with HSP is one of the reasons for the reduction of IL-10 expression in B cells.

[Application of reflux symptom index in diagnosis of allergic patients with laryngopharyngeal reflux]

Objective:To explore the diagnostic value and optimal diagnostic threshold of reflux symptom index(RSI) in allergic patients with laryngopharyngeal reflux. Method: All the adult allergic patients with respiratory tract symptoms completed the RSI with the consent of the patients. A total of 150 patients with RSI＞13 were screened out. The LPR patients were confirmed by 24 h pH-metry of pharyngo-laryngoesophageal (allergic group). The same number of non allergic laryngeal reflux patients were selected as control group (non allergic group). The ratio of RSI＞13 to LPR was calculated. The total score of RSI and each score were compared between the allergic group and the non allergic group. ROC curve was used to analyze the highly suspicious RSI score thresholds for patients with reflux laryngitis. Result:Only 53(35.33%) of 150 patients with RSI＞13 were diagnosed as LPR after 24 h pH-metry test in allergic patients. Among the 9 symptoms of RSI, the scores of 6 symptoms in allergic group were significantly higher than those in non allergic group(P<0.05). The average RSI score of allergic group was 23.57±3.17. The average RSI score of non allergic group was 17.57±2.64. The total score of allergic group was higher than that of non allergic group(P<0.05). According to the RSI score ROC curve of allergic group, the area under 95% confidence interval curve was 0.815. RSI had certain diagnostic accuracy for allergic patients with LPR. The best critical value of RSI score for allergic patients with LPR was 18, the sensitivity was 94.3%, and the specificity was 56.7%. Conclusion:RSI can be used to screen allergic patients with LPR, diagnostic score threshold RSI＞18 points, has a certain diagnostic accuracy.

[Correlation between both neck/shoulder and low back pain and daily behavioral habits among middle school students in Shenzhen]

Objective: To study the relations between neck/shoulder or low back pain and their daily behavioral habits among middle school students in Shenzhen. Methods: We randomly chose 3 952 students from 10 high schools in Shenzhen to complete the questionnaires. Data was gathered and analyzed, using the IBM SPSS 23.0. Results: Of the 3 952 participants, 20.3% had neck/shoulder pain and 15.2% had low back pain. Among students experienced neck/shoulder pain, female (25.3%), high school (24.5%) and boarding students (24.4%) experienced higher rates of neck/shoulder pain (P<0.05). Female students (17.9%) also had higher rate of low back pain (P<0.05). Results from logistic regression analysis showed that factors as: gender, type of school, taking naps on the desk, staying up late, self-perceived stress from learning, overloading homework, time spent on mobile phone and TV, spending long time on computer etc. were related to the neck/shoulder pain (P<0.05). Factors as: gender, naps on the desk, stay up late, self-perceived stress, overloading homework, time spent on mobile phone and TV etc., were related to low back pain (P<0.05). Conclusion: Neck/shoulder pain and low back pain were both commonly seen while high self-perceived stress, sedentary behaviors and poor sleeping habits were associated with both neck/shoulder and low back pain in high school students in Shenzhen.

Ultralow-Temperature Thermal Conductivity of the Kitaev Honeycomb Magnet α-RuCl_{3} across the Field-Induced Phase Transition

Recently, there have been increasingly hot debates on whether there exists a quantum spin liquid in the Kitaev honeycomb magnet α-RuCl_{3} in a high magnetic field. To investigate this issue, we perform ultralow-temperature thermal conductivity measurements on single crystals of α-RuCl_{3} down to 80 mK and up to 9 T. Our experiments clearly show a field-induced phase transition occurring at μ_{0}H_{c}≈7.5  T, above which the magnetic order is completely suppressed. The minimum of thermal conductivity at 7.5 T is attributed to the strong scattering of phonons by magnetic fluctuations. Most importantly, above 7.5 T, we do not observe any significant contribution of thermal conductivity from gapless magnetic excitations, which puts a strong constraint on the nature of the high-field phase of α-RuCl_{3}.

Winding paths to simplicity: genome evolution in facultative insect symbionts

Symbiosis between organisms is an important driving force in evolution. Among the diverse relationships described, extensive progress has been made in insect–bacteria symbiosis, which improved our understanding of the genome evolution in host-associated bacteria. Particularly, investigations on several obligate mutualists have pushed the limits of what we know about the minimal genomes for sustaining cellular life. To bridge the gap between those obligate symbionts with extremely reduced genomes and their non-host-restricted ancestors, this review focuses on the recent progress in genome characterization of facultative insect symbionts. Notable cases representing various types and stages of host associations, including those from multiple genera in the family Enterobacteriaceae (class Gammaproteobacteria), Wolbachia (Alphaproteobacteria) and Spiroplasma (Mollicutes), are discussed. Although several general patterns of genome reduction associated with the adoption of symbiotic relationships could be identified, extensive variation was found among these facultative symbionts. These findings are incorporated into the established conceptual frameworks to develop a more detailed evolutionary model for the discussion of possible trajectories. In summary, transitions from facultative to obligate symbiosis do not appear to be a universal one-way street; switches between hosts and lifestyles (e.g. commensalism, parasitism or mutualism) occur frequently and could be facilitated by horizontal gene transfer.

This review synthesizes the recent progress in genome characterization of insect-symbiotic bacteria, the emphases include (i) patterns of genome organization, (ii) evolutionary models and trajectories, and (iii) comparisons between facultative and obligate symbionts.

[Strategy for minimally invasive cochlear implantation and residual hearing preservation]

In the past few decades, considerable development was achieved in the cochlear implantation following the emergence of innovative electrode array and advances in minimally invasive surgery. Minimally invasive technique led to a better preservation of residual low-frequency hearing. The loss of residual hearing was caused by complicated factors. According to previous studies, a slower and stable speed of electrode insertion and the use of perioperative steroids were demonstrated to have a positive impact on hearing preservation. The selection of electrode array or its insertion approaches didn't show any distinctive benefits in hearing preservation.

A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-l-proline

The human microbiome encodes vast numbers of uncharacterized enzymes, limiting our functional understanding of this community and its effects on host health and disease. By incorporating information about enzymatic chemistry into quantitative metagenomics, we determined the abundance and distribution of individual members of the glycyl radical enzyme superfamily among the microbiomes of healthy humans. We identified many uncharacterized family members, including a universally distributed enzyme that enables commensal gut microbes and human pathogens to dehydrate trans-4-hydroxy-l-proline, the product of the most abundant human posttranslational modification. This "chemically guided functional profiling" workflow can therefore use ecological context to facilitate the discovery of enzymes in microbial communities.

Optical directional amplification in a three-mode optomechanical system

We study the directional amplification of an optical probe field in a three-mode optomechanical system, where the mechanical resonator interacts with two linearly-coupled optical cavities and the cavities are driven by strong optical pump fields. The optical probe field is injected into one of the cavity modes, and at the same time, the mechanical resonator is subject to a mechanical drive with the driving frequency equal to the frequency difference between the optical probe and pump fields. We show that the transmission of the probe field can be amplified in one direction and de-amplified in the opposite direction. This directional amplification or de-amplification results from the constructive or destruction interference between different transmission paths in this three-mode optomechanical system.

Complete chloroplast genome sequence of common bermudagrass (Cynodon dactylon (L.) Pers.) and comparative analysis within the family Poaceae

Common bermudagrass (Cynodon dactylon (L.) Pers.) belongs to the subfamily Chloridoideae of the Poaceae family, one of the most important plant families ecologically and economically. This grass has a long connection with human culture but its systematics is relatively understudied. In this study, we sequenced and investigated the chloroplast genome of common bermudagrass, which is 134,297 bp in length with two single copy regions (LSC: 79,732 bp; SSC: 12,521 bp) and a pair of inverted repeat (IR) regions (21,022 bp). The annotation contains a total of 128 predicted genes, including 82 protein-coding, 38 tRNA, and 8 rRNA genes. Additionally, our in silico analyses identified 10 sets of repeats longer than 20 bp and predicted the presence of 36 RNA editing sites. Overall, the chloroplast genome of common bermudagrass resembles those from other Poaceae lineages. Compared to most angiosperms, the accD gene and the introns of both clpP and rpoC1 genes are missing. Additionally, the ycf1, ycf2, ycf15, and ycf68 genes are pseudogenized and two genome rearrangements exist. Our phylogenetic analysis based on 47 chloroplast protein-coding genes supported the placement of common bermudagrass within Chloridoideae. Our phylogenetic character mapping based on the parsimony principle further indicated that the loss of the accD gene and clpP introns, the pseudogenization of four ycf genes, and the two rearrangements occurred only once after the most recent common ancestor of the Poaceae diverged from other monocots, which could explain the unusual long branch leading to the Poaceae when phylogeny is inferred based on chloroplast sequences.

[Analysis of the SLC26A4 mutation from 230 deafness patients in Guangxi region]

Objective:To investigate the mutation characteristics of SLC26A4 gene from 230 hearing loss patients in Guangxi region.Method:Two hundred thirty patients with hearing loss were enrolled in the study. Eight mutation sites in SLC26A4 gene were tested; the types of gene mutation and the inner ear CT features of the mutationpositive patients were analyzed.Result:Among 230 deafness patients,the total mutation rate of SLC26A4 gene is 2.61%(6/230). The types of gene mutation include SLC26A4 IVS7-2A> G heterozygous in 2 case(0.87%).1226G> A homozygous in 1 cases(0.43%),IVS7-2A>G，IVS11+47T>C and 1548insC mutations in 2 cases(0.87%).Conclusion:The mutation rate of SLC26A4 gene in Guangxi region is lower than the national average level. The main mutation type in Guangxi region is SLC26A4 IVS7 2A>G. In this study, two gene mutations (SLC26A4 IVS11+47T> C and 1548insC) are firstly found, suggesting that some rare mutation types of SLC26A4 may exist in patients living in Guangxi region.

Electrophysiological Effects of Dexmedetomidine on Sinoatrial Nodes of Rabbits

BACKGROUND

The purpose of this study was to investigate the electrophysiological effects of dexmedetomidine on pacemaker cells in sinoatrial nodes of rabbits.

METHODS

Healthy rabbits were anesthetized intravenously with sodium pentobarbital, and the hearts were quickly dissected and mounted in a tissue bath. Machine-pulled glass capillary microelectrodes which were connected to a high input impedance amplifier and impaled in dominant pacemaker cells. Thereafter, an intracellular microelectrode technique was used to record action potential.

RESULTS

The amplitude of action potential, velocity of diastolic (phase 4) depolarization, and rate of pacemaker firing in normal pacemaker cells in sinoatrial node were decreased by use of dexmedetomidine (0.5 ng/ml, 5 ng/ml, 50 ng/ml) in a concentration-dependent manner. Pretreatment with yohimbine (1 μM), did not alter the effects of dexmedetomidine (5 ng/ml) on sinoatrial node pacemaker cells. Pretreatment with CsCl (2 mmol/L), dexmedetomidine (5 ng/ml) decreased the amplitude of action potential, but had no significant effect on other parameters of action potential.

CONCLUSIONS

Dexmedetomidine exerts inhibitory electrophysiological effects on pacemaker cells in sinoatrial nodes of rabbits in a concentration-dependent manner, which may not be mediated by alpha 2-adrenoreceptor.

KEY WORDS

Action potential; Cardiology; Dexmedetomidine; Pacemaker activity; Sinoatrial node.

Serum Irisin Level is Higher and Related with Insulin in Acanthosis Nigricans-related Obesity

OBJECTIVE

Acanthosis nigricans (AN) is proved to be a skin phenotype of hyperinsulinemia especially in obese patients. Irisin is a new myokine which plays an important role in metabolic disorders, such as obesity, insulin resistance, and type 2 diabetes. The role of irisin in the development of AN-related obesity is not yet understood. In this study, we aimed to investigate the relationship between irisin and AN-related obesity. Patients & Measurements: 30 obese patients without AN (OB group), 30 obese patients with AN (AN group), and 20 age-matched healthy volunteers (control group, CON) were included in this study. Weight, BMI, lipid profile, FFA, UA, and CRP were measured in all participants. Oral Glucose Tolerance tests (OGTT) were performed and serum glucose and plasma insulin were measured at 0, 30, 60,120 and 180 min. The AUC (area under curve) of glucose and insulin was calculated. Serum irisin was measured by ELISA.

RESULTS

Hyperinsulinemia is found in both AN and OB groups. The AN group had higher levels of insulin but better blood glucose tolerance and insulin response. The difference in irisin levels between the 3 groups was statistically significant, with the AN group showing the highest serum level of irisin. Serum irisin levels were positively correlated with BMI, and fasting insulin.

CONCLUSION

AN is a state of hyperinsulinmia and has better insulin response and glucose tolerance compared to obese patients without AN. Serum irisin may be a protective factor against impaired beta cell function in obesity with AN.

Detection of methemoglobin in whole blood based on confocal micro-Raman spectroscopy and multivariate statistical techniques

Raman spectroscopy has been shown to have the potential for revealing oxygenated and spin ability of hemoglobin. In this study, confocal micro-Raman spectroscopy is developed to monitor the effect of sodium nitrite on oxyhemoglobin (HbO2 ) in whole blood. We observe that the band at 1,638 cm(-1) which is sensitive to the oxidation state decreases dramatically, while the 1,586 cm(-1) (low-spin state band) reduces both in methemoglobin (MetHb) and poisoning blood. Our results show that adding in sodium nitrite lead to the transition from HbO2 (Fe(2+) ) to MetHb (Fe(3+) ) in whole blood, and the iron atom converts from the low spin state to the high spin state with a delocalization from porphyrin plane. Moreover, multivariate statistical techniques, including principal components analysis (PCA) and linear discriminant analysis (LDA) are employed to develop effective diagnostic algorithms for classification of spectra between pure blood and poisoning blood. The diagnostic algorithms based on PCA-LDA yield a diagnostic sensitivity of 100% and specificity of 100% for separating poisoning blood from normal blood. Receiver operating characteristic (ROC) curve further confirms the effectiveness of the diagnostic algorithm based on PCA-LDA technique. The results from this study demonstrate that Raman spectroscopy combined with PCA-LDA algorithms has tremendous potential for the non-invasive detection of nitrite poisoning blood.

Distinct and concurrent pathways of Pol II- and Pol IV-dependent siRNA biogenesis at a repetitive trans-silencer locus in Arabidopsis thaliana

Short interfering RNAs (siRNAs) homologous to transcriptional regulatory regions can induce RNA-directed DNA methylation (RdDM) and transcriptional gene silencing (TGS) of target genes. In our system, siRNAs are produced by transcribing an inverted DNA repeat (IR) of enhancer sequences, yielding a hairpin RNA that is processed by several Dicer activities into siRNAs of 21-24 nt. Primarily 24-nt siRNAs trigger RdDM of the target enhancer in trans and TGS of a downstream GFP reporter gene. We analyzed siRNA accumulation from two different structural forms of a trans-silencer locus in which tandem repeats are embedded in the enhancer IR and distinguished distinct RNA polymerase II (Pol II)- and Pol IV-dependent pathways of siRNA biogenesis. At the original silencer locus, Pol-II transcription of the IR from a 35S promoter produces a hairpin RNA that is diced into abundant siRNAs of 21-24 nt. A silencer variant lacking the 35S promoter revealed a normally masked Pol IV-dependent pathway that produces low levels of 24-nt siRNAs from the tandem repeats. Both pathways operate concurrently at the original silencer locus. siRNAs accrue only from specific regions of the enhancer and embedded tandem repeat. Analysis of these sequences and endogenous tandem repeats producing siRNAs revealed the preferential accumulation of siRNAs at GC-rich regions containing methylated CG dinucleotides. In addition to supporting a correlation between base composition, DNA methylation and siRNA accumulation, our results highlight the complexity of siRNA biogenesis at repetitive loci and show that Pol II and Pol IV use different promoters to transcribe the same template.

Influences of species mixture on biomass of Masson pine (Pinus massoniana Lamb) forests

The effect of tree diversity on productivity in subtropical forests in China is poorly understood. We investigated the biomasses of trees, understory vegetation, coarse roots, and fine roots with varying proportions of Pinus massoniana, mixed with other tree species in stands of the same age, to examine the effects of tree diversity. With an increase of P. massoniana proportion, the tree and understory biomasses increased at first, and then gradually decreased. As expected, the biomass of fine roots decreased with soil depth. Stands with 40 to 60% P. massoniana had the highest biomass, whereas stands with <20% P. massoniana had the least biomass. Stands with <20% P. massoniana had the least understory biomass, whereas those with 20 to 40% Masson pine had the least fine root biomass.

Complete sequence and comparative analysis of the chloroplast genome of coconut palm (Cocos nucifera)

Coconut, a member of the palm family (Arecaceae), is one of the most economically important trees used by mankind. Despite its diverse morphology, coconut is recognized taxonomically as only a single species (Cocos nucifera L.). There are two major coconut varieties, tall and dwarf, the latter of which displays traits resulting from selection by humans. We report here the complete chloroplast (cp) genome of a dwarf coconut plant, and describe the gene content and organization, inverted repeat fluctuations, repeated sequence structure, and occurrence of RNA editing. Phylogenetic relationships of monocots were inferred based on 47 chloroplast protein-coding genes. Potential nodes for events of gene duplication and pseudogenization related to inverted repeat fluctuation were mapped onto the tree using parsimony criteria. We compare our findings with those from other palm species for which complete cp genome sequences are available.

Chloroplast phylogenomics indicates that Ginkgo biloba is sister to cycads

Molecular phylogenetic studies have not yet reached a consensus on the placement of Ginkgoales, which is represented by the only living species, Ginkgo biloba (common name: ginkgo). At least six discrepant placements of ginkgo have been proposed. This study aimed to use the chloroplast phylogenomic approach to examine possible factors that lead to such disagreeing placements. We found the sequence types used in the analyses as the most critical factor in the conflicting placements of ginkgo. In addition, the placement of ginkgo varied in the trees inferred from nucleotide (NU) sequences, which notably depended on breadth of taxon sampling, tree-building methods, codon positions, positions of Gnetopsida (common name: gnetophytes), and including or excluding gnetophytes in data sets. In contrast, the trees inferred from amino acid (AA) sequences congruently supported the monophyly of a ginkgo and Cycadales (common name: cycads) clade, regardless of which factors were examined. Our site-stripping analysis further revealed that the high substitution saturation of NU sequences mainly derived from the third codon positions and contributed to the variable placements of ginkgo. In summary, the factors we surveyed did not affect results inferred from analyses of AA sequences. Congruent topologies in our AA trees give more confidence in supporting the ginkgo-cycad sister-group hypothesis.

The complete chloroplast genome of Ginkgo biloba reveals the mechanism of inverted repeat contraction

We determined the complete chloroplast genome (cpDNA) of Ginkgo biloba (common name: ginkgo), the only relict of ginkgophytes from the Triassic Period. The cpDNA molecule of ginkgo is quadripartite and circular, with a length of 156,945 bp, which is 6,458 bp shorter than that of Cycas taitungensis. In ginkgo cpDNA, rpl23 becomes pseudo, only one copy of ycf2 is retained, and there are at least five editing sites. We propose that the retained ycf2 is a duplicate of the ancestral ycf2, and the ancestral one has been lost from the inverted repeat A (IR_A). This loss event should have occurred and led to the contraction of IRs after ginkgos diverged from other gymnosperms. A novel cluster of three transfer RNA (tRNA) genes, trnY-AUA, trnC-ACA, and trnSeC-UCA, was predicted to be located between trnC-GCA and rpoB of the large single-copy region. Our phylogenetic analysis strongly suggests that the three predicted tRNA genes are duplicates of trnC-GCA. Interestingly, in ginkgo cpDNA, the loss of one ycf2 copy does not significantly elevate the synonymous rate (Ks) of the retained copy, which disagrees with the view of Perry and Wolfe (2002) that one of the two-copy genes is subjected to elevated Ks when its counterpart has been lost. We hypothesize that the loss of one ycf2 is likely recent, and therefore, the acquired Ks of the retained copy is low. Our data reveal that ginkgo possesses several unique features that contribute to our understanding of the cpDNA evolution in seed plants.

Large positive and negative lateral shifts near pseudo-Brewster dip on reflection from a chiral metamaterial slab

The lateral shifts from a slab of lossy chiral metamaterial are predicted for both perpendicular and parallel components of the reflected field, when the transverse electric (TE)-polarized incident wave is applied. By introducing different chirality parameter, the lateral shifts can be large positive or negative near the pseudo-Brewster angle. It is found that the lateral shifts from the negative chiral slab are affected by the angle of incidence and the chirality parameter. In the presence of inevitable loss of the chiral slab, the enhanced lateral shifts will be decreased, and the pseudo-Brewster angle will disappear correspondingly. For the negative chiral slab with loss which is invisible for the right circularly polarized (RCP) wave, we find that the loss of the chiral slab will lead to the fluctuation of the lateral shift with respect to the thickness of the chiral slab.The validity of the stationary-phase analysis is demonstrated by numerical simulations of a Gaussian-shaped beam.

Micro-Raman spectroscopy of algae: composition analysis and fluorescence background behavior

Preliminary feasibility studies were performed using Stokes Raman scattering for compositional analysis of algae. Two algal species, Chlorella sorokiniana (UTEX #1230) and Neochloris oleoabundans (UTEX #1185), were chosen for this study. Both species were considered to be candidates for biofuel production. Raman signals due to storage lipids (specifically triglycerides) were clearly identified in the nitrogen-starved C. sorokiniana and N. oleoabundans, but not in their healthy counterparts. On the other hand, signals resulting from the carotenoids were found to be present in all of the samples. Composition mapping was conducted in which Raman spectra were acquired from a dense sequence of locations over a small region of interest. The spectra obtained for the mapping images were filtered for the wavelengths of characteristic peaks that correspond to components of interest (i.e., triglyceride or carotenoid). The locations of the components of interest could be identified by the high intensity areas in the composition maps. Finally, the time evolution of fluorescence background was observed while acquiring Raman signals from the algae. The time dependence of fluorescence background is characterized by a general power law decay interrupted by sudden high intensity fluorescence events. The decreasing trend is likely a result of photo-bleaching of cell pigments due to prolonged intense laser exposure, while the sudden high intensity fluorescence events are not understood.