Constructing Cooperative Interface via Bi-Functional COF for Facilitating the Sulfur Conversion and Li+ Dynamics.

Lithium-sulfur (Li-S) batteries stand out for their high theoretical specific capacity and cost-effectiveness. However, the practical implementation of Li-S batteries is hindered by issues such as the shuttle effect, tardy redox kinetics, and dendrite growth. Herein, an appealingly designed covalent organic framework (COF) with bi-functional active sites of cyanide groups and polysulfide chains (COF-CN-S) is developed as cooperative functional promoters to simultaneously address dendrites and shuttle effect issues. Combining in situ techniques and theoretical calculations, it can be demonstrated that the unique chemical architecture of COF-CN-S is capable of performing the following functions: 1) The COF-CN-S delivers significantly enhanced Li+ transport capability due to abundant ion-hopping sites (cyano-groups); 2) it functions as a selective ion sieve by regulating the dynamic behavior of polysulfide anions and Li+ , thus inhibiting shuttle effect and dendrite growth; 3) by acting as a redox mediator, the COF-CN-S can effectively control the electrochemical behavior of polysulfides and enhance their conversion kinetics. Based on the above advantages, the COF-CN-S endows Li-S batteries with excellent performance. This study highlights the significance of interface modification and offers novel insights into the rational design of organic materials in the Li-S realm.

Integrated transcriptome and physiological analysis revealed core transcription factors that promote flavonoid biosynthesis in apricot in response to pathogenic fungal infection.

MAIN CONCLUSION: Integrated transcriptome and physiological analysis of apricot leaves after Fusarium solani treatment. In addition, we identified core transcription factors and flavonoid-related synthase genes which may function in apricot disease resistance. Apricot (Prunus armeniaca) is an important economic fruit species, whose yield and quality of fruit are limited owing to its susceptibility to diseases. However, the molecular mechanisms underlying the response of P. armeniaca to diseases is still unknown. In this study, we used physiology and transcriptome analysis to characterize responses of P. armeniaca subjected to Fusarium solani. The results showed increasing malondialdehyde (MDA) content, enhanced peroxidase (POD) and catalase (CAT) activity during F. solani infestation. A large number of differentially expressed genes (DEGs), which included 4281 upregulated DEGs and 3305 downregulated DEGs, were detected in P. armeniaca leaves exposed to F. solani infestation. Changes in expression of transcription factors (TFs), including bHLH, AP2/ERF, and WRKY indicated their role in triggering pathogen-responsive genes in P. armeniaca. During the P. armeniaca response to F. solani infestation, the content of total flavonoid was changed, and we identified enzyme genes associated with flavonoid biosynthesis. Ectopic overexpression of PabHLH15 and PabHLH102 in Nicotiana benthamiana conferred elevated resistance to Fspa_1. Moreover, PabHLH15 and PabHLH102 positively interact with the promoter of flavonoid biosynthesis-related genes. A regulatory network of TFs regulating enzyme genes related to flavonoid synthesis affecting apricot disease resistance was constructed. These results reveal the potential underlying mechanisms of the F. solani response of P. armeniaca, which would help improve the disease resistance of P. armeniaca and may cultivate high-quality disease-resistant varieties in the future.

Diurnal Regulation of Leaf Photosynthesis Is Related to Leaf-Age-Dependent Changes in Assimilate Accumulation in Camellia oleifera.

In order to clarify the mechanism of diurnal changes in photosynthesis of leaves of different leaf ages in Camellia oleifera, current-year leaves (CLs) and annual leaves (ALs) were used as the test materials to analyze the diurnal changes in photosynthetic parameters, assimilate contents and enzyme activities, as well as structural differences and expression levels of sugar transport regulating genes. The rate of net photosynthesis in CLs and ALs was highest in the morning. During the day, there was a decrease in the CO2 assimilation rate, and this decrease was greater in ALs than in CLs at midday. The maximal efficiency of photosystem II (PSII) photochemistry (Fv/Fm) showed a decreasing trend as the sunlight intensity increased, but no significant difference between CLs and ALs was found. Compared with CLs, ALs showed a greater decrease in the carbon export rate at midday and the levels of sugars and starch increased significantly in ALs, accompanied by higher enzyme activity of sucrose synthetase and ADP-glucose pyrophosphorylase. In addition, compared with CLs, ALs had a larger leaf vein area and higher leaf vein density, as well as higher expression levels of sugar transport regulating genes during the day. It is concluded that the excessive accumulation of assimilate is an important factor contributing to the midday depression of photosynthesis in Camellia oleifera annual leaves on a sunny day. Sugar transporters may play an important regulatory role in excessive accumulation of assimilate in leaves.

One-Step Calcination Synthesis of Bulk-Doped Surface-Modified Ni-Rich Cathodes with Superlattice for Long-Cycling Li-Ion Batteries.

Nickel-rich (Ni≥90 %) layered cathodes are critical materials for achieving higher-energy-density and lower-cost next-generation Li-ion batteries (LIBs). However, their bulk and interface structural instabilities significantly impair their electrochemical performance, thus hindering their widespread adoption in commercial LIBs. Exploiting Ti and Mo diffusion chemistry, we report one-step calcination to synthesize bulk-to-surface modified LiNi0.9 Co0.09 Mo0.01 O2 (NCMo90) featuring a 5 nm Li2 TiO3 coating on the surface, a Mo-rich Li+ /Ni2+ superlattice at the sub-surface, and Ti-doping in the bulk. Such a multi-functional structure effectively maintains its structural integrity upon cycling. As a result, such NCMo90 exhibits a high initial capacity of 221 mAh g-1 at 0.1 C, excellent rate performance (184 mAh g-1 at 5 C), and high capacity retention of 94.0 % after 500 cycles. This work opens a new avenue to developing industry-applicable Ni-rich cathodes for next-generation LIBs.

Low Light Facilitates Cyclic Electron Flows around PSI to Assist PSII against High Temperature Stress.

Photosystem II (PSII) of grapevine leaves is easily damaged under heat stress, but no such injury is observed when the leaves are heated in low light. To elucidate the mechanisms, we compared the photosynthetic characteristics of grapevine seedlings under heat treatments (42 °C) for 4 h in the dark or low light (200 µmol m-2 s-1). At 42 °C in the dark, the PSII maximum quantum yield (Fv/Fm) decreased significantly with the increase in time but did not change much in low light. The JIP (chlorophyll a fluorescence rise kinetics) test results showed that low light significantly alleviated the damage to the oxygen evolving complexes (OECs; the K-step was less visible) by heat stress. Further, in the presence of de novo D1 protein synthesis inhibitor chloramphenicol, Fv/Fm did not differ significantly between dark and light treatments under heat stress. The 50% re-reduction (RR50) of P700+ on cessation of far-red illumination was faster after light treatment than that in the dark. After exposure to 25 °C in a low light for 15 min, Y(NO) (the constitutive non-regulatory non-photochemical quenching) treated by heat stress and darkness was higher than that by heat stress and light. Overall, our results suggested that enhanced CEFs around PSI in low light could assist PSII against heat damage by maintaining the rate of PSII repair and inhibiting the non-radiative charge recombination in PSII reaction centers.

Understanding a Single-Li-Ion COF Conductor for Being Dendrite Free in a Li-Organic Battery.

In addition to improving ion conductivity and the transference number, single-Li-ion conductors (SLCs) also enable the elimination of interfacial side reactions and concentration difference polarization. Therefore, the SLCs can achieve high performance in solid-state batteries with Li metal as anode and organic molecule as cathode. Covalent organic frameworks (COFs) are leading candidates for constructing SLCs because of the excellent 1D channels and accurate chemical-modification skeleton. Herein, various contents of lithium-sulfonated covalently anchored COFs (denoted as LiO3S-COF1 and LiO3S-COF2) are controllably synthesized as SLCs. Due to the directional ion channels, high Li contents, and single-ion frameworks, LiO3S-COF2 shows exceptional Li-ion conductivity of 5.47 × 10-5 S · cm-1, high transference number of 0.93, and low activation energy of 0.15 eV at room temperature. Such preeminent Li-ion-transported properties of LiO3S-COF2 permit stable Li+ plating/stripping in a symmetric lithium metal battery, effectively impeding the Li dendrite growth in a liquid cell. Moreover, the designed quasi-solid-state cell (organic anthraquinone (AQ) as cathode, Li metal as anode, and LiO3S-COF2 as electrolyte) shows high-capacity retention and rate behavior. Consequently, LiO3S-COF2 implies a potential value restraining the dissolution of small organic molecules and Li dendrite growth.

Ni3FeN functionalized carbon nanofibers boosting polysulfide conversion for Li-S chemistry.

Limiting the shuttle effect of polysulfides is an important means to realizing high energy density lithium-sulfur batteries (Li-S). In this study, an efficient electrocatalyst (CNFs@Ni3FeN) is synthesized by anchoring Ni3FeN in the carbon nanofibers (CNFs). The CNFs@Ni3FeN shows electrocatalytic activity and enhances the conversion of polysulfides. After assembling a battery, a high initial capacity (1452 mA h g-1) and favorable long-time cycling stability (100 cycles) with a capacity retention rate of 83% are obtained by the electrocatalysis of Ni3FeN. Compared with unmodified CNFs, the cycling stability of CNFs@Ni3FeN can be greatly improved. The catalytic mechanism is further deduced by X-ray photoelectron spectroscopy (XPS). Our work will inspire the rational design of CNFs@support hybrids for various electrocatalysis applications.

Heat-induced down-regulation of photosystem II protects photosystem I in honeysuckle (Lonicera japonica).

Honeysuckle (Lonicera japonica Thunb.) is a traditional medicinal plant in China which is often threatened by high temperature at midday during summer. Heat-induced effects on the photosynthetic apparatus in honeysuckle are associated with a depression of the photosystem II (PSII) photochemical efficiency. However, very limited information is available on regulation of photosynthetic electron flow in PSI photoprotection in heat-stressed honeysuckle. Simultaneous analyses of chlorophyll fluorescence and the change in absorbance of P700 showed that energy transformation and electron transfer activity in PSII decreased under heat stress, but the fraction of photo-oxidizable PSI (Pm) remained stable. With treatments at 38 and 42 °C, the photochemical electron transport in PSII was suppressed, whereas the cyclic electron flow (CEF) around PSI was induced. In addition, the levels of high energy state quenching (qE) and P700 oxidation increased significantly with increasing temperature. However, a decline of qE in antimycin A (AA)- or 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU)-treated leaves after heat treatment was observed, while P700 oxidation decreased only in the presence of AA. The results indicate that heat-induced inhibition of PSII and induction of CEF cooperatively protect PSI from ROS damages through moderate down-regulation of photosynthetic electron flow from PSII to PSI.

The complete chloroplast genome sequences of an endangered orchid species Paphiopedilum parishii (Orchidaceae).

Paphiopedilum parishii (Rchb. f.) Stein is an endangered and rare species with highly ornamental value. In this study, we report the complete chloroplast genome of P. parishii using the Illumina sequencing data. The total genome of P. parishii is 154,689 bp in length and the GC content is 35.9%, with a pair of inverted repeats (IRs) regions of 32,690 bp each, a large single-copy region (LSC) of 86,863 bp and a small single-copy region (SSC) of 2,446 bp. The chloroplast genome encoded 127 genes, including 82 protein-coding genes (CDS), 8 rRNA genes and 37 tRNA genes. The phylogenetic tree showed that P. parishii was clustered with other species in Paphiopedilum with strong support based on the complete chloroplast genome.

Direct and Indirect Somatic Embryogenesis Induction in Camellia oleifera Abel.

Camellia oleifera Abel. is an important woody oil species; however, the shortage of rapid and industrialized seedling culture is a large constraint on the development of the tea oil industry. Somatic embryogenesis (SE) is one of the main powerful biotechnological tools for plant mass regeneration, but the largely unknown SE in C. oleifera limits the scale production of clonal plants. In this study, we described a high-efficiency SE system via direct and indirect pathways in C. oleifera and investigated the effect of genotype, explant age and phytohormones on SE. In the direct pathway, somatic embryos were highly induced from immature seeds 220 days after full blossom, and the development of embryoids was achieved with a combination of 0.19 mg/L 2,4-dichlorophenoxyacetic acid (2,4-D) and 0.05 mg/L thidiazuron (TDZ). In the indirect pathway, embryogenic calli were induced from the same explants in medium containing 1.5 mg/L 2,4-D, while 0.75 mg/L 2,4-D treatment led to high proliferation rates for embryogenic calli. The addition of 0.19 mg/L 2,4-D alone stimulated the production of globular embryos while causing a 75% loss of the induction rate in the heart embryo stage. Upon transfer of the globular embryos to phytohormone-free medium, an optimal induction rate of 62.37% from globular embryos to cotyledonary embryos was obtained. These data suggest that the subsequent differentiation process after the globular embryo stage in ISE is more similar to an endogenous phytohormones-driven process. Mature embryos germinated to produce intact plantlets on half-strength MS basal medium with a regeneration rate of 63.67%. Histological analysis confirmed the vascular bundle isolation of embryoids from the mother tissue. We further studied the different varieties and found that there were no significant genotype differences for SE induction efficiency in C. oleifera. Thus, we established a high-efficiency induction system for direct and indirect somatic embryogenesis (ISE) in C. oleifera and regenerated intact plantlets via SE, not organogenesis. ISE has a more complicated induction and regulatory mechanism than direct somatic embryogenesis. The improved protocol of SE would benefit mass propagation and genetic manipulation in C. oleifera.

Stimulation of cyclic electron flow around PSI as a response to the combined stress of high light and high temperature in grape leaves.

Changes in cyclic electron flow (CEF) around PSI activity after exposing grape (Vitis vinifera L.) seedling leaves to the combined stress of high temperature (HT) and high light (HL) were investigated. The PSII potential quantum efficiency (Fv/Fm) decreased significantly under exposure to HT, and this decrease was greater when HT was combined with HL, whereas the PSI activity maintained stable. HT enhanced CEF mediated by NAD(P)H dehydrogenase remarkably. Compared with the control leaves, the half-time of P700+ re-reduction decreased during the HT treatment; this decrease was even more pronounced under the combined stress, implying significantly enhanced CEF as a result of the treatment. However, the heat-induced increase in nonphotochemical quenching (NPQ) was greater under HL, accompanied by a greater enhancement in high-energy state quenching. These results suggest that the combined stress of HT and HL resulted in severe PSII photoinhibition, whereas CEF showed plasticity in its response to environmental stress and played an important role in PSII and PSI photoprotection through accelerating generation of the thylakoid proton gradient and the induction of NPQ.

Induction of cyclic electron flow around photosystem I during heat stress in grape leaves.

Photosystem II (PSII) in plants is susceptible to high temperatures. The cyclic electron flow (CEF) around PSI is thought to protect both PSII and PSI from photodamage. However, the underlying physiological mechanisms of the photosynthetic electron transport process and the role of CEF in grape at high temperatures remain unclear. To investigate this issue, we examined the responses of PSII energy distribution, the P700 redox state and CEF to high temperatures in grape leaves. After exposing 'Cabernet Sauvignon' leaves to various temperatures (25, 30, 35, 40 and 45°C) in the light (600µmol photons m-2s-1) for 4h, the maximum quantum yield of PSII (Fv/Fm) significantly decreased at high temperatures (40 and 45°C), while the maximum photo-oxidizable P700 (Pm) was not affected. As the temperature increased, higher initial rates of increase in post-illumination Chl fluorescence were detected, which were accompanied by an increase in high energy state quenching (qE). The chloroplast NAD(P)H dehydrogenase-dependent CEF (NDH-dependent CEF) activities were different among grape cultivators. 'Gold Finger' with greater susceptibility to photoinhibition, exhibited lower NDH-dependent CEF activities under acute heat stress than a more heat tolerant 'Cabernet Sauvignon'. These results suggest that overclosure of PSII reaction centers at high temperature resulted in the photoinhibition of PSII, while the stimulation of CEF in grape played an important role in the photoprotection of PSII and PSI at high temperatures through contributing to the generation of a proton gradient.

Extraction and isolation of flavonoid glycosides from Flos Sophorae Immaturus using ultrasonic-assisted extraction followed by high-speed countercurrent chromatography.

A method of ultrasonic-assisted extraction followed by high-speed countercurrent chromatography was established for the extraction and isolation of three flavonoid glycosides, i.e. rutin, narcissin, and nicotiflorin from Flos Sophorae Immaturus. The effects of ultrasonic-assisted extraction factors for the main flavonoid compound (rutin) from Flos Sophorae Immaturus were optimized using Box-Behnken design combined with response surface methodology. The optimum conditions were determined as ultrasonic power 83% (600 W), solvent-to-material ratio 56:1, methanol concentration 82% v/v, and extraction time 60 min. Three bioactive flavonol glucosides, rutin, narcissin, and nicotiflorin were isolated from Flos Sophorae Immaturus using high-speed countercurrent chromatography. The separation was performed with a two-phase solvent system containing ethyl acetate/n-butanol/methanol/water (4:0.9:0.2:5, v/v). Amounts of 87 mg of rutin, 10.8 mg of narcissin, and 1.8 mg of nicotiflorin were isolated from 302 mg of crude extract of Flos Sophorae Immaturus in a one-step separation within 160 min with purities of 99.3, 98.0, and 95.1%, respectively, as determined by HPLC with diode array detection. Their structures were characterized by UV, MS, and NMR spectroscopy. It was demonstrated that the established method was simple, fast, and convenient, which was feasible to extract and isolate active flavonoid glycosides from Flos Sophorae Immaturus.

Contribution of dfrA and inhA mutations to the detection of isoniazid-resistant Mycobacterium tuberculosis isolates.

Screening of 127 isoniazid (INH)-resistant Mycobacterium tuberculosis isolates from Singapore for mutations within the dfrA and inhA genes revealed mutations in 0 and 5 (3.9%) isolates respectively, implying that mutations in dfrA do not contribute to the detection of INH-resistant M. tuberculosis and that mutations within inhA are rare. Thirty-seven (29%) of the 127 isolates had no mutations in any of the genes implicated in INH resistance (katG, kasA, and ndh; inhA and ahpC promoters), suggesting that there are new INH targets yet to be discovered.

IL-1beta, IL-6, and RANTES as biomarkers of Chikungunya severity.

BACKGROUND: Little is known about the immunopathogenesis of Chikungunya virus. Circulating levels of immune mediators and growth factors were analyzed from patients infected during the first Singaporean Chikungunya fever outbreak in early 2008 to establish biomarkers associated with infection and/or disease severity. METHODS AND FINDINGS: Adult patients with laboratory-confirmed Chikungunya fever infection, who were referred to the Communicable Disease Centre/Tan Tock Seng Hospital during the period from January to February 2008, were included in this retrospective study. Plasma fractions were analyzed using a multiplex-microbead immunoassay. Among the patients, the most common clinical features were fever (100%), arthralgia (90%), rash (50%) and conjunctivitis (40%). Profiles of 30 cytokines, chemokines, and growth factors were able to discriminate the clinical forms of Chikungunya from healthy controls, with patients classified as non-severe and severe disease. Levels of 8 plasma cytokines and 4 growth factors were significantly elevated. Statistical analysis showed that an increase in IL-1beta, IL-6 and a decrease in RANTES were associated with disease severity. CONCLUSIONS: This is the first comprehensive report on the production of cytokines, chemokines, and growth factors during acute Chikungunya virus infection. Using these biomarkers, we were able to distinguish between mild disease and more severe forms of Chikungunya fever, thus enabling the identification of patients with poor prognosis and monitoring of the disease.

T-cell receptor-gamma gene analysis in evolving to advancing cutaneous T-cell lymphoma.

The diagnosis of cutaneous T-cell lymphoma is often a challenge for the dermatopathologist. Early stages can mimic inflammatory dermatoses. Our aim was to explore the applicability of a standard T-cell receptor-gamma polymerase chain reaction in various subtypes of cutaneous T-cell lymphomas. Ninety-six biopsy specimens from 38 patients were selected. These included 72 specimens of mycosis fungoides, 12 specimens of non-mycosis fungoides T-cell lymphomas, and 12 specimens in which histology was non-specific or equivocal in patients who were later diagnosed to have lymphoma. T-cell clones were detected in 53 of 72 specimens of mycosis fungoides and eight of 12 specimens of non-mycosis fungoides lymphomas. Of the 72 specimens of mycosis fungoides, T-cell clones were detected in eight of 10 specimens of mycosis fungoides-associated follicular mucinosis and pigmented purpura-like mycosis fungoides. Four specimens from the 12 prediagnostic for cutaneous T-cell lymphomas showed presence of T-cell clones, identical to subsequent clones detected when lymphoma was fully established. In specimens where histology is not diagnostic and T-cell receptor-gamma gene analysis is positive, patients should be followed up closely. T-cell receptor-gamma gene analysis is a useful adjunct to histological diagnosis of early stage and variant types of mycosis fungoides.

Tuberculosis associated with Mycobacterium tuberculosis Beijing and non-Beijing genotypes: a clinical and immunological comparison.

BACKGROUND: The Mycobacterium tuberculosis Beijing genotype is biologically different from other genotypes. We aimed to clinically and immunologically compare human tuberculosis caused by Beijing and non-Beijing strains. METHODS: Pulmonary tuberculosis patients were prospectively enrolled and grouped by their M. tuberculosis genotypes. The clinical features, plasma cytokine levels, and cytokine gene expression levels in peripheral blood mononuclear cells (PBMC) were compared between the patients in Beijing and non-Beijing groups. RESULTS: Patients in the Beijing group were characterized by significantly lower frequency of fever (odds ratio, 0.12, p = 0.008) and pulmonary cavitation (odds ratio, 0.2, p = 0.049). Night sweats were also significantly less frequent by univariate analysis, and the duration of cough prior to diagnosis was longer in Beijing compared to non-Beijing groups (medians, 60 versus 30 days, p = 0.048). The plasma and gene expression levels of interferon (IFN) gamma and interleukin (IL)-18 were similar in the two groups. However, patients in the non-Beijing group had significantly increased IL-4 gene expression (p = 0.018) and lower IFN-gamma : IL-4 cDNA copy number ratios (p = 0.01). CONCLUSION: Patients with tuberculosis caused by Beijing strains appear to be less symptomatic than those who have disease caused by other strains. Th1 immune responses are similar in patients infected with Beijing and non-Beijing strains, but non-Beijing strains activate more Th2 immune responses compared with Beijing strains, as evidenced by increased IL-4 expression.

Mimotopes for lupus-derived anti-DNA and nucleosome-specific autoantibodies selected from random peptide phage display libraries: facts and follies.

Autoantibodies against chromatin are the most characteristic serological feature in SLE patients. Anti-dsDNA and nucleosome-specific antibodies are associated with glomerulonephritis, the most serious manifestation of SLE. Identification of peptides mimicking conformational epitopes (so-called mimotopes) on the nucleosome recognized by these antibodies is of considerable interest. Using an approach similar to that used previously to characterize mimotopes for anti-DNA autoantibodies, we have selected and identified a mimotope for a nucleosome-specific autoantibody (#32) by screening a random peptide phage display library. However, the reactivity of monoclonal antibody (mAb) #32 with the selected mimotope (MIMO#0) in ELISA was dependent on the blocking reagents used. Using nonfat dry milk (5%), mAb #32 clearly bound to MIMO#0, but using fetal bovine calf serum (FCS) (5%), there was no binding. Furthermore, again dependent on the blocking reagent used in ELISA, the selected mimotope MIMO#0 was not only recognized by the selecting antibody mAb #32, but also by a large number of other monoclonal anti-DNA, anti-histone and nucleosome-specific autoantibodies (NSA). We could demonstrate that the selected mimotope was able to bind directly to nucleosomal material (DNA/histone complexes) and labeled DNA. This finding was extended to other previously identified mimotopes for anti-DNA autoantibodies. We conclude that nucleosomal material (DNA/histone complexes), derived from reagents used during the mimotope selection procedure, resulted in the selection of DNA-binding peptides from the phage display library, rather than mimotopes. In addition, we could demonstrate that blocking reagents greatly influence the reactivity of anti-DNA, anti-histone and nucleosome-specific autoantibodies in ELISA. Development of blocking reagents devoid of nucleosomal material (DNA/histone complexes) is urgently needed for assay systems in which anti-nuclear autoantibodies are tested.

Characterization of ancestral Mycobacterium tuberculosis by multiple genetic markers and proposal of genotyping strategy.

Sixty-eight ancestral Mycobacterium tuberculosis isolates were previously identified by using the tuberculosis-specific deletion 1 (TbD1) PCR and mycobacterial interspersed-repetitive-unit-variable-number tandem repeat (MIRU-VNTR) typing (Y. J. Sun, R. Bellamy, A. S. G. Lee, S. T. Ng, S. Ravindran, S.-Y. Wong, C. Locht, P. Supply, and N. I. Paton, J. Clin. Microbiol. 42:1986-1993, 2004). These TbD1(+) ancestral isolates were further characterized and typed in this study by IS6110 restriction fragment length polymorphism (RFLP) typing, VNTR typing using exact tandem repeats (VNTR-ETR), and spoligotyping of the direct-repeat region. To our knowledge, this is the first characterization of this genogroup by multiple genetic markers based on a fairly large sample size. In this genogroup, all spoligotypes were characterized by the absence of spacers 29 to 32 and 34. In addition, VNTR-ETR typing could add further resolution to the clustered isolates identified by MIRU-VNTR, and the combination of MIRU-VNTR and VNTR-ETR, called MIRU-ETR, showed the highest discriminatory power for these strains compared to IS6110 RFLP typing and spoligotyping alone. However, MIRU-ETR appeared to still cluster some probably epidemiologically unrelated strains, as judged by IS6110 RFLP divergence. Therefore, a typing strategy based on stepwise combination of MIRU-ETR and IS6110 RFLP is proposed to achieve maximal discrimination for unrelated TbD1(+) strains. This typing strategy may be useful in areas where TbD1(+) ancestral strains are prevalent.

Use of mycobacterial interspersed repetitive unit-variable-number tandem repeat typing to examine genetic diversity of Mycobacterium tuberculosis in Singapore.

Strain typing using variable-number tandem repeats of mycobacterial interspersed repetitive units (MIRU-VNTR) is a powerful tool for studying the epidemiology and genetic relationships of Mycobacterium tuberculosis isolates. For this study, isolates from 291 patients in Singapore were genotyped by this method. One hundred sixty-six distinct MIRU-VNTR patterns were detected. One hundred sixty-two strains were grouped into 1 of 35 different MIRU-VNTR clusters and 131 isolates were unique. In this sample collection, 9 of the 12 MIRU-VNTR loci were moderately or highly discriminative according to their allelic diversities. The Hunter-Gaston discriminatory index was 0.975, indicating the high power of discrimination of MIRU-VNTR typing. By direct comparisons with previously typed MIRU-VNTR patterns and by genetic relationship analyses, we could identify and clearly define four epidemic groups of M. tuberculosis in our sample, corresponding to the W/Beijing, East-Africa-Indian, Haarlem, and Delhi genotype families. Furthermore, MIRU-VNTR typing was able to clearly distinguish ancestral and modern M. tuberculosis strains as defined by TbD1 genomic deletion analysis. These results indicate that MIRU-VNTR typing can be a useful first-line tool for studying the genetic diversity of M. tuberculosis isolates in a large urban setting such as Singapore.