Phylogenetic position of Cyperus clandestinus (Cypereae,Cyperaceae) clarified by morphological and molecular evidence

Extreme morphological reduction and convergent evolution can obscure taxonomic relationships. This phenomenon is frequently encountered in Cyperaceae, where characters traditionally used to diagnose genera have been shown to have evolved independently multiple times. The Ethiopian high‐altitude perennial first described as Cyperus clandestinus was subsequently moved to Ficinia because it has spiral glume arrangement, unlike typical Cyperus species, which have distichous glume arrangement. However, this position has remained uncertain as no nutlets have previously been studied to establish the presence or absence of the gynophore – the synapomorphy for Ficinia. We resolve this 140‐year‐old puzzle by describing the morphology of the nutlet, which lacks a gynophore, and use DNA sequence data to resolve the taxon within Cyperus. Cyperus clandestinus was found to be closely related to Remirea maritima and Cyperus cyperoides in the C₄Cyperus clade, whose members predominantly have distichously arranged glumes. This provides further evidence for the unreliability of glume arrangement as a character to distinguish between members of the Cyperus and Ficinia clades, whereas gynophore presence is more congruent with molecular data.     

Differences in polypeptide expression in thermoinhibited and germinating achenes of Tagetes minuta L.

When imbibed at their optimum germination temperature of25°C, achenes of Tagetes minutaL.germinate over a period of 48 h. At a temperature of36°C, the achenes become thermoinhibited and do notgerminate. This elevated temperature does not harm the achenes, however, and assoon as the temperature is reduced below 35°C,germination occurs, but is spread over a reduced period of only 24h. The polypeptide patterns of germinating and thermoinhibitedachenes were compared, to test whether thermoinhibition is the result ofdifferential gene expression or repression. Ten polypeptides which weredifferentially expressed in thermoinhibited achenes were observed. Thesepolypeptides were all extremely specific to thermoinhibited achenes anddeclinedrapidly when the incubation temperature was decreased, in a manner whichcorrelated with the increase in germinability of the achenes. The tightlyregulated nature of the expression of these polypeptides suggests thatthermoinhibition in T. minuta may be under positivecontrol. These proteins may therefore result in the prevention of radicleemergence at unfavourable temperatures.     

Plasma Levels of Middle Molecules to Estimate Residual Kidney Function in Haemodialysis without Urine Collection

Background

Residual Kidney Function (RKF) is associated with survival benefits in haemodialysis (HD) but is difficult to measure without urine collection. Middle molecules such as Cystatin C and β2-microglobulin accumulate in renal disease and plasma levels have been used to estimate kidney function early in this condition. We investigated their use to estimate RKF in patients on HD.

Design

Cystatin C, β2-microglobulin, urea and creatinine levels were studied in patients on incremental high-flux HD or hemodiafiltration(HDF). Over sequential HD sessions, blood was sampled pre- and post-session 1 and pre-session 2, for estimation of these parameters. Urine was collected during the whole interdialytic interval, for estimation of residual GFR (GFR_Residual = mean of urea and creatinine clearance). The relationships of plasma Cystatin C and β2-microglobulin levels to GFR_Residual and urea clearance were determined.

Results

Of the 341 patients studied, 64% had urine output>100ml/day, 32.6% were on high-flux HD and 67.4% on HDF. Parameters most closely correlated with GFR_Residual were 1/β2-micoglobulin (r² 0.67) and 1/Cystatin C (r² 0.50). Both these relationships were weaker at low GFR_Residual. The best regression model for GFR_Residual, explaining 67% of the variation, was: GFRResidual=160.3⋅(1β2m)−4.2 Where β2m is the pre-dialysis β2 microglobulin concentration (mg/L). This model was validated in a separate cohort of 50 patients using Bland-Altman analysis. Areas under the curve in Receiver Operating Characteristic analysis aimed at identifying subjects with urea clearance≥2ml/min/1.73m² was 0.91 for β2-microglobulin and 0.86 for Cystatin C. A plasma β2-microglobulin cut-off of ≤19.2mg/L allowed identification of patients with urea clearance ≥2ml/min/1.73m² with 90% specificity and 65% sensitivity.

Conclusion

Plasma pre-dialysis β2-microglobulin levels can provide estimates of RKF which may have clinical utility and appear superior to cystatin C. Use of cut-off levels to identify patients with RKF may provide a simple way to individualise dialysis dose based on RKF.     

Evidence of Long-Lived Founder Virus in Mother-to-Child HIV Transmission

Exposure of the infant’s gut to cell-associated and cell-free HIV-1 trafficking in breast milk (BM) remains a primary cause of mother-to-child transmission (MTCT). The mammary gland represents a unique environment for HIV-1 replication and host-virus interplay. We aimed to explore the origin of the virus transmitted during breastfeeding, and the link with quasi-species found in acellular and cellular fractions of breast-milk (BM) and in maternal plasma. The C2–V5 region of the env gene was amplified, cloned and sequenced from the RNA and DNA of BM, the RNA from the mother’s plasma (PLA) and the DNA from infant’s dried blood spot (DBS) in 11 post-natal mother-infant pairs. Sequences were assembled in Geneious, aligned in ClustalX, manually edited in SeAL and phylogenetic reconstruction was undertaken in PhyML and MrBayes. We estimated the timing of transmission (ETT) and reconstructed the time for the most recent common ancestor (TMRCA) of the infant in BEAST. Transmission of single quasi-species was observed in 9 of 11 cases. Phylogenetic analysis illustrated a BM transmission event by cell-free virus in 4 cases, and by cell-associated virus in 2 cases but could not be identified in the remaining 5 cases. Molecular clock estimates, of the infant ETT and TMRCA, corresponded well with the timing of transmission estimated by sequential infant DNA PCR in 10 of 11 children. The TMRCA of BM variants were estimated to emerge during gestation in 8 cases. We hypothesize that in the remaining cases, the breast was seeded with a long-lived lineage latently infecting resting T-cells. Our analysis illustrated the role of DNA and RNA virus in MTCT. We postulate that DNA archived viruses stem from latently infected quiescent T-cells within breast tissue and MTCT can be expected to continue, albeit at low levels, should interventions not effectively target these cells.     

Inactivation of arginine esterase E-I of Bitis gabonica venom by irreversible inhibitors including a water-soluble carbodiimide, a chloromethyl ketone and isatoic anhydride.

1. Esterase E-I from Bitis gabonica was inactivated with irreversible inhibitors which included studies with a water-soluble carbodiimide, an affinity labelling peptide and a mechanism-based inactivator. 2. The reaction with 1-ethyl-3(3-dimethylaminopropyl)-carbodiimide was biphasic and the dominant part followed saturation kinetics. At pH 5.5 a rate constant of 0.4 min-1 for inactive enzyme formation was calculated and a dissociation constant (Ki) of 0.2 M for the enzyme-inhibitor complex. 3. Inactivation with D-Phe-Pro-Arg-chloromethyl ketone indicated a two-step mechanism, for which the reaction parameters at pH 8.0 were determined. The Ki value was 0.2 microM and the inactivation rate was 2.5 min-1. 4. With isatoic anhydride pseudo-first-order kinetics was observed. At pH 8.0 a rate constant of 0.9 min-1 and a Ki of 2.0 mM were obtained. The inactivation of the enzyme was found to be governed by a group in the enzyme showing a pK value of 7.3.