Concentration of Lymph Node Aspirate Improves the Sensitivity of Acid Fast Smear Microscopy for the Diagnosis of Tuberculous Lymphadenitis in Jimma,Southwest Ethiopia

Background

Tuberculous lymphadenitis (TBLN) is the most common form of extrapulmonary tuberculosis. The cytomorphological features of lymph node smears have reduced specificity for the diagnosis of tuberculosis. The diagnosis of TBLN with direct smear microscopy lacks sensitivity due to the limited number of bacilli in lymph node aspirate. Therefore, we aimed to assess whether the concentration of lymph node aspirate improves the sensitivity of acid fast smear microscopy for the diagnosis of tuberculous lymphadenitis.

Methods

A cross-sectional comparative study was conducted on 200 patients clinically suspected for tuberculous lymphadenitis in Jimma, Ethiopia. Lymph node aspirate was collected. The first two drops were used for cytomorphological study and direct acid fast staining. The remaining aspirate was treated with N-acetyl-L-cysteine (NALC) and concentrated by centrifugation at 3000 g for 15 minutes. The sediment was used for acid fast staining and culture. Differentiation of M. tuberculosis complex (MTBC) from non-tuberculous mycobacteria (NTM) was done by para-nitrobenzoic acid susceptibility test.

Result

Complete data were available for 187 study subjects. 68% (127/187) were positive for M. tuberculosis on culture. Four isolates, 2.1% (4/187), were identified as NTM. The detection rate of direct smear microscopy was 25.1% and that of the concentration method 49.7%. Cytomorphologically, 79.7% of cases were classified as TBLN. The sensitivity of direct smear microscopy was 34.6%, for concentrated smear microscopy 66.1%, and for cytomorphology 89.8%. Two AFB positive cases on concentration method were non-tuberculosis mycobacteria (NTM). The concentration method yielded a positive result from seven cases diagnosed as suppurative abscess by cytology. Both for the direct and concentration methods the highest rate of AFB positivity was observed in smears showing caseous necrosis alone. Smear positivity rate decreased with the appearance of epithelioid cell aggregates.

Conclusion

The concentration of lymph node aspirates for acid fast smear microscopy had significantly higher sensitivity than direct microscopy.     

The role of conserved waters in conformational transitions of Q61H K-ras

To investigate the stability and functional role of long-residence water molecules in the Q61H variant of the signaling protein K-ras, we analyzed all available Ras crystal structures and conformers derived from a series of independent explicit solvent molecular dynamics (MD) simulations totaling 1.76 μs. We show that the protein samples a different region of phase space in the presence and absence of several crystallographically conserved and buried water molecules. The dynamics of these waters is coupled with the local as well as the global motions of the protein, in contrast to less buried waters whose exchange with bulk is only loosely coupled with the motion of loops in their vicinity. Aided by two novel reaction coordinates involving the distance (d) between the C(α) atoms of G60 at switch 2 and G10 at the P-loop and the N-C(α)-C-O dihedral (ξ) of G60, we further show that three water molecules located in lobe1, at the interface between the lobes and at lobe2, are involved in the relative motion of residues at the two lobes of Q61H K-ras. Moreover, a d/ξ plot classifies the available Ras x-ray structures and MD-derived K-ras conformers into active GTP-, intermediate GTP-, inactive GDP-bound, and nucleotide-free conformational states. The population of these states and the transition between them is modulated by water-mediated correlated motions involving the functionally critical switch 2, P-loop and helix 3. These results suggest that water molecules act as allosteric ligands to induce a population shift among distinct switch 2 conformations that differ in effector recognition.     

Western Honeybee Drones and Workers (Apis mellifera ligustica) Have Different Olfactory Mechanisms than Eastern Honeybees (Apis cerana cerana)

The honeybees Apis mellifera ligustica (Aml) and Apis cerana cerana (Acc) are two different western and eastern bee species that evolved in distinct ecologies and developed specific antennal olfactory systems for their survival. Knowledge of how their antennal olfactory systems function in regards to the success of each respective bee species is scarce. We compared the antennal morphology and proteome between respective sexually mature drones and foraging workers of both species using a scanning electron microscope, two-dimensional electrophoresis, mass spectrometry, bioinformatics, and quantitative real-time polymerase chain reaction. Despite the general similarities in antennal morphology of the drone and worker bees between the two species, a total of 106 and 100 proteins altered their expression in the drones' and the workers' antennae, respectively. This suggests that the differences in the olfactory function of each respective bee are supported by the change of their proteome. Of the 106 proteins that altered their expression in the drones, 72 (68%) and 34 (32%) were overexpressed in the drones of Aml and Acc, respectively. The antennae of the Aml drones were built up by the highly expressed proteins that were involved in carbohydrate metabolism and energy production, molecular transporters, antioxidation, and fatty acid metabolism in contrast to the Acc drones. This is believed to enhance the antennal olfactory functions of the Aml drones as compared to the Acc drones during their mating flight. Likewise, of the 100 proteins with expression changes between the worker bees of the two species, 67% were expressed in higher levels in the antennae of Aml worker contrasting to 33% in the Acc worker. The overall higher expressions of proteins related to carbohydrate metabolism and energy production, molecular transporters, and antioxidation in the Aml workers compared with the Acc workers indicate the Aml workers require more antennal proteins for their olfactory mechanisms to perform efficient foraging activities than do the Acc worker bees. These data decipher the mechanisms of the western and eastern drone and worker bees acting in response to their different olfactory system in their distinct ecosystem.     

Coherent Control of Gap Plasmons of a Complex Nanosystem by Shaping Driving Femtosecond Pulses

Geometry-based control of local field of coupled plasmonic nanostructures is efficient for optimization of the field intensity. However, it provides weak control over spatial and temporal dynamics of the field and thus unsuitable for experimental studies and practical applications where fixed geometries are needed. In this study, we report on pulsed excitation of strongly coupled plasmonic nanosystem comprised of nanorod and split-ring antenna. The near-field intensities are manipulated by controlling time delay, relative phase, and polarization of the ultrafast excitation pulses. We show that the spectral and spatial intensities of the local fields at the gap regions of the coupled nanosystem can be pronounced by using two identical pulses with least time delay and phase difference. The corresponding temporal intensities of electric near-fields for both parallel and orthogonal polarization of the illumination fields are also briefly discussed. These findings might have implications for controlled excitation of complexly coupled plasmonic nanosystems.     

Association of trace metal elements with lipid profiles in type 2 diabetes mellitus patients: a cross sectional study

Background

It is well known that dyslipidemia and chronic hyperglycemia increase the onset of diabetes and diabetic complication. The aim of this study is to see the association of trace metals elements and lipid profile among type 2 diabetes mellitus patients.

Methods

The study was conducted on 214 type 2 diabetic patients at Jimma University Specialized Hospital, Jimma, Ethiopia. All the eligible study participants responded to the structured interviewer administered questionnaire and fasting venous blood was drawn for biochemical analysis. Trace metal elements (zinc(Zn⁺²), magnesium(Mg⁺²), chromium(Cr⁺³), calcium(Ca⁺²), phosphorus(Po₄ ^?3), manganese(Mn⁺²), copper(Cu⁺²), and iron(Fe⁺³)) and lipid profiles (total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein (HDL-C), and triglycerides (TG)) were measured by atomic absorption spectrophotometry and enzymatic determination method respectively. Data were analyzed by SPSS version 24 software for windows. Bonferroni correction for multiple statistical comparisons was used and a p-value less than 0.01 were accepted as a level of significance.

Result

The mean age of study participants was 42.95(±12.6) with an average of 5.83(±3.1) years being diagnosed with diabetes mellitus. The BMI of female (27.1(±4.9)) was significantly higher than male (25.21(±4.2)). BMI shows positive and significant (p < 0.01) association with lipid profiles (TC, LDL-C, and TG) among type 2 diabetic patients in the liner regression model. In addition, WH-R was positively associated with TG. In Pearson partial correlation adjusted for sex and age, Za⁺² shown to have statistically significant and negative correlations with TC, LDL-C and with TG. Mg⁺² and Cr⁺² negatively and significantly correlated with the lipid profile TC and LDL-C. Ca⁺² negatively correlated with TC and TG. Po^?3 ₄ positively correlated with HDL-C; iron negatively correlated with TC. However, in the liner regression model, only calcium positively and significantly (Beta = ?0.21, p < 0.01) associated with TG.

Conclusion

In the current study, a negative correlation was observed between trace metal elements (Zn⁺², Mg⁺², Cr⁺³, Ca⁺² and Fe⁺³) and lipid profile (TC, LDL-C and TG) among type 2 diabetes mellitus patients. In addition, Ca⁺² observed to be associated with TG. Future studies are highly advised to uncover the bidirectional association between trace metal element and dyslipidemia in diabetic patients.

     

Prenatal fortified balanced energy-protein supplementation and birth outcomes in rural Burkina Faso: A randomized controlled efficacy trial

BackgroundProviding balanced energy–protein (BEP) supplements is a promising intervention to improve birth outcomes in low- and middle-income countries (LMICs); however, evidence is limited. We aimed to assess the efficacy of fortified BEP supplementation during pregnancy to improve birth outcomes, as compared to iron–folic acid (IFA) tablets, the standard of care.Methods and findingsWe conducted an individually randomized controlled efficacy trial (MIcronutriments pour la SAnté de la Mère et de l’Enfant [MISAME]-III) in 6 health center catchment areas in rural Burkina Faso. Pregnant women, aged 15 to 40 years with gestational age (GA) <21 completed weeks, were randomly assigned to receive either fortified BEP supplements and IFA (intervention) or IFA (control). Supplements were provided during home visits, and intake was supervised on a daily basis by trained village-based project workers. The primary outcome was prevalence of small-for-gestational age (SGA) and secondary outcomes included large-for-gestational age (LGA), low birth weight (LBW), preterm birth (PTB), gestational duration, birth weight, birth length, Rohrer’s ponderal index, head circumference, thoracic circumference, arm circumference, fetal loss, and stillbirth. Statistical analyses followed the intention-to-treat (ITT) principle. From October 2019 to December 2020, 1,897 pregnant women were randomized (960 control and 937 intervention). The last child was born in August 2021, and birth anthropometry was analyzed from 1,708 pregnancies (872 control and 836 intervention). A total of 22 women were lost to follow-up in the control group and 27 women in the intervention group. BEP supplementation led to a mean 3.1 percentage points (pp) reduction in SGA with a 95% confidence interval (CI) of −7.39 to 1.16 (P = 0.151), indicating a wide range of plausible true treatment efficacy. Adjusting for prognostic factors of SGA, and conducting complete cases (1,659/1,708, 97%) and per-protocol analysis among women with an observed BEP adherence ≥75% (1,481/1,708, 87%), did not change the results. The intervention significantly improved the duration of gestation (+0.20 weeks, 95% CI 0.05 to 0.36, P = 0.010), birth weight (50.1 g, 8.11 to 92.0, P = 0.019), birth length (0.20 cm, 0.01 to 0.40, P = 0.044), thoracic circumference (0.20 cm, 0.04 to 0.37, P = 0.016), arm circumference (0.86 mm, 0.11 to 1.62, P = 0.025), and decreased LBW prevalence (−3.95 pp, −6.83 to −1.06, P = 0.007) as secondary outcomes measures. No differences in serious adverse events [SAEs; fetal loss (21 control and 26 intervention) and stillbirth (16 control and 17 intervention)] between the study groups were found. Key limitations are the nonblinded administration of supplements and the lack of information on other prognostic factors (e.g., infection, inflammation, stress, and physical activity) to determine to which extent these might have influenced the effect on nutrient availability and birth outcomes.ConclusionsThe MISAME-III trial did not provide evidence that fortified BEP supplementation is efficacious in reducing SGA prevalence. However, the intervention had a small positive effect on other birth outcomes. Additional maternal and biochemical outcomes need to be investigated to provide further evidence on the overall clinical relevance of BEP supplementation.Trial registrationClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT03533712","term_id":"NCT03533712"}}NCT03533712.

Brenda de Kok and colleagues investigate the efficacy of fortified BEP supplementation during pregnancy to improve birth outcomes, as compared to iron-folic acid (IFA) tablets, among pregnant women in rural Burkina Faso.     

Population viability analysis of Walia ibex (Capra walie) at Simien Mountains National Park (SMNP), Ethiopia

Population viability analysis (PVA) has been applied to the management of many threatened populations. The objective of this study was, therefore, to estimate the PVA of Walia ibex at the Simen Mountains National Park, in the north‐central highlands of Ethiopia, with respect to population growth parameters, the probability of the population reaching a lower extinction threshold and the mean time to extinction. Direct census of the population was carried out in 2009. Secondary census data were also collected from park authorities and the literature reviews. The result revealed that the estimates of the infinitesimal mean, μ (0.04117) was greater than the infinitesimal variance, σ² (0.0219). The probability that the population reaches the extinction threshold was very low (0.15%). The mean time required for the counts to decline from the existing population size to one individual animal was 160 years. But threatened species are adversely affected by changes in landscape. These changes can be brought by short‐ and long‐term human and climate change impacts, respectively. Therefore, with the absence of environmental and demographic stochasticity and, with the application of appropriate reproductions and habitat management, the population of Walia ibex will be viable and reaches its mean time of extinctions after 160 years.     

Calculation of protein ionization equilibria with conformational sampling: pK(a) of a model leucine zipper, GCN4 and barnase.

The use of conformational ensembles provided by nuclear magnetic resonance (NMR) experiments or generated by molecular dynamics (MD) simulations has been regarded as a useful approach to account for protein motions in the context of pK(a) calculations, yet the idea has been tested occasionally. This is the first report of systematic comparison of pK(a) estimates computed from long multiple MD simulations and NMR ensembles. As model systems, a synthetic leucine zipper, the naturally occurring coiled coil GCN4, and barnase were used. A variety of conformational averaging and titration curve-averaging techniques, or combination thereof, was adopted and/or modified to investigate the effect of extensive global conformational sampling on the accuracy of pK(a) calculations. Clustering of coordinates is proposed as an approach to reduce the vast diversity of MD ensembles to a few structures representative of the average electrostatic properties of the system in solution. Remarkable improvement of the accuracy of pK(a) predictions was achieved by the use of multiple MD simulations. By using multiple trajectories the absolute error in pK(a) predictions for the model leucine zipper was reduced to as low as approximately 0.25 pK(a) units. The validity, advantages, and limitations of explicit conformational sampling by MD, compared with the use of an average structure and a high internal protein dielectric value as means to improve the accuracy of pK(a) calculations, are discussed.     

Dynamics of the acetylcholinesterase tetramer

Acetylcholinesterase rapidly hydrolyzes the neurotransmitter acetylcholine in cholinergic synapses, including the neuromuscular junction. The tetramer is the most important functional form of the enzyme. Two low-resolution crystal structures have been solved. One is compact with two of its four peripheral anionic sites (PAS) sterically blocked by complementary subunits. The other is a loose tetramer with all four subunits accessible to solvent. These structures lacked the C-terminal amphipathic t-peptide (WAT domain) that interacts with the proline-rich attachment domain (PRAD). A complete tetramer model (AChEt) was built based on the structure of the PRAD/WAT complex and the compact tetramer. Normal mode analysis suggested that AChEt could exist in several conformations with subunits fluctuating relative to one another. Here, a multiscale simulation involving all-atom molecular dynamics and Cα-based coarse-grained Brownian dynamics simulations was carried out to investigate the large-scale intersubunit dynamics in AChEt. We sampled the ns-μs timescale motions and found that the tetramer indeed constitutes a dynamic assembly of monomers. The intersubunit fluctuation is correlated with the occlusion of the PAS. Such motions of the subunits “gate” ligand-protein association. The gates are open more than 80% of the time on average, which suggests a small reduction in ligand-protein binding. Despite the limitations in the starting model and approximations inherent in coarse graining, these results are consistent with experiments which suggest that binding of a substrate to the PAS is only somewhat hindered by the association of the subunits.     

Synthesis and structure-activity relationship of N-alkyl Gly-boro-Pro inhibitors of DPP4, FAP, and DPP7

The structure-activity relationship of various N-alkyl Gly-boro-Pro derivatives against three dipeptidyl peptidases (DPPs) was studied. In a series of N-cycloalkyl analogs, DPP4 and fibroblast activation protein-alpha (FAP) optimally preferred N-cycloheptyl whereas DPP7 tolerated even larger cycloalkyl rings. Gly alpha-carbon derivatization of N-cyclohexyl or N-(2-adamantyl) Gly-boro-Pro resulted in a significant decrease in potency against all the three DPPs.