Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition.

BACKGROUND: Comparisons of traditional hunter-gatherers and pre-agricultural communities in Africa with urban and suburban Western North American and European cohorts have clearly shown that diet, lifestyle and environment are associated with gut microbiome composition. Yet, little is known about the gut microbiome composition of most communities in the very diverse African continent. South Africa comprises a richly diverse ethnolinguistic population that is experiencing an ongoing epidemiological transition and concurrent spike in the prevalence of obesity, largely attributed to a shift towards more Westernized diets and increasingly inactive lifestyle practices. To characterize the microbiome of African adults living in more mainstream lifestyle settings and investigate associations between the microbiome and obesity, we conducted a pilot study, designed collaboratively with community leaders, in two South African cohorts representative of urban and transitioning rural populations. As the rate of overweight and obesity is particularly high in women, we collected single time-point stool samples from 170 HIV-negative women (51 at Soweto; 119 at Bushbuckridge), performed 16S rRNA gene sequencing on these samples and compared the data to concurrently collected anthropometric data. RESULTS: We found the overall gut microbiome of our cohorts to be reflective of their ongoing epidemiological transition. Specifically, we find that geographical location was more important for sample clustering than lean/obese status and observed a relatively higher abundance of the Melainabacteria, Vampirovibrio, a predatory bacterium, in Bushbuckridge. Also, Prevotella, despite its generally high prevalence in the cohorts, showed an association with obesity. In comparisons with benchmarked datasets representative of non-Western populations, relatively higher abundance values were observed in our dataset for Barnesiella (log2fold change (FC) = 4.5), Alistipes (log2FC = 3.9), Bacteroides (log2FC = 4.2), Parabacteroides (log2FC = 3.1) and Treponema (log2FC = 1.6), with the exception of Prevotella (log2FC = - 4.7). CONCLUSIONS: Altogether, this work identifies putative microbial features associated with host health in a historically understudied community undergoing an epidemiological transition. Furthermore, we note the crucial role of community engagement to the success of a study in an African setting, the importance of more population-specific studies to inform targeted interventions as well as present a basic foundation for future research.

Using BpyAla to generate copper artificial metalloenzymes: a catalytic and structural study.

Artificial metalloenzymes (ArMs) have emerged as a promising avenue in the field of biocatalysis, offering new reactivity. However, their design remains challenging due to the limited understanding of their protein dynamics and how the introduced cofactors alter the protein scaffold structure. Here we present the structures and catalytic activity of novel copper ArMs capable of (R)- or (S)-stereoselective control, utilizing a steroid carrier protein (SCP) scaffold. To incorporate 2,2'-bipyridine (Bpy) into SCP, two distinct strategies were employed: either Bpy was introduced as an unnatural amino acid (2,2'-bipyridin-5-yl)alanine (BpyAla) using amber stop codon expression or via bioconjugation of bromomethyl-Bpy to cysteine residues. The resulting ArMs proved to be effective at catalysing an enantioselective Friedel-Crafts reaction with SCP_Q111BpyAla achieving the best selectivity with an enantioselectivity of 72% ee (S). Interestingly, despite using the same protein scaffold, different attachment strategies for Bpy at the same residue (Q111) led to a switch in the enantiopreference of the ArM. X-ray crystal structures of SCP_Q111CBpy and SCP_Q111BpyAla ArMs with bound Cu(ii) ions unveiled crucial differences in the orientation of the catalytic centre. Combining structural information, alanine scanning studies, and computational analysis shed light on the distinct active sites of the ArMs, clarifying that these active sites stabilise the nucleophilic substrate on different sides of the electrophile leading to the observed switch in enantioselectivity. This work underscores the importance of integrating structural studies with catalytic screening to unravel the intricacies of ArM behaviour and facilitate their development for targeted applications in biocatalysis.

Long-range interaction between heterogeneously charged membranes.

Despite their neutrality, surfaces or membranes with equal amounts of positive and negative charge can exhibit long-range electrostatic interactions if the surface charge is heterogeneous; this can happen when the surface charges form finite-size domain structures. These domains can be formed in lipid membranes where the balance of the different ranges of strong but short-ranged hydrophobic interactions and longer-ranged electrostatic repulsion result in a finite, stable domain size. If the domain size is large enough, oppositely charged domains in two opposing surfaces or membranes can be strongly correlated by the electrostatic interactions; these correlations give rise to an attractive interaction of the two membranes or surfaces over separations on the order of the domain size. We use numerical simulations to demonstrate the existence of strong attractions at separations of tens of nanometers. Large line tensions result in larger domains but also increase the charge density within the domain. This promotes correlations and, as a result, increases the intermembrane attraction. On the other hand, increasing the salt concentration increases both the domain size and degree of domain anticorrelation, but the interactions are ultimately reduced due to increased screening. The result is a decrease in the net attraction as salt concentration is increased.

Hybrid lipids as a biological surface-active component.

Cell membranes contain small domains (on the order of nanometers in size, sometimes called rafts) of lipids whose hydrocarbon chains are more ordered than those of the surrounding bulk-phase lipids. Whether these domains are fluctuations, metastable, or thermodynamically stable, is still unclear. Here, we show theoretically how a lipid with one saturated hydrocarbon chain that prefers the ordered environment and one partially unsaturated chain that prefers the less ordered phase, can act as a line-active component. We present a unified model that treats the lipids in both the bulk and at the interface and show how they lower the line tension between domains, eventually driving it to zero at sufficiently large interaction strengths or at sufficiently low temperatures. In this limit, finite-sized domains stabilized by the packing of these hybrid lipids can form as equilibrium structures.

Heterodimerization studies of calix[4]arene derivatives in polar solvents.

[reaction: see text] Several calix[4]arene derivatives propylated on the lower rim and substituted on the upper rim with amino or carboxyl groups have been synthesized. Examples include calixarenes substituted with alanino (C- and N-linked), amino, carboxy, carboxyphenyl, and amidino groups. The self-assembly of these derivatized calixarenes into heterodimers has been studied by NMR in DMSO-d(6) or CD(3)OD with 5% aqueous phosphate buffer.

Neoplasms in young dogs after perinatal irradiation.

For a study of the life-time effects of irradiation during development, 1,680 beagles were given single, whole-body exposures to 60Co gamma-radiation at one of three prenatal (preimplantation, embryonic, and fetal) or at one of three postnatal (neonatal, juvenile, and young adult) ages. Mean doses were 0, 0.16, or 0.83 Gy. For comparison with data on childhood cancer after prenatal irradiation, examination was made of tumors occurring in young dogs in this life-span experiment. Up to 4 years of age, 18 dogs had neoplasms diagnosed, 2 of these being in controls. Four dogs that were irradiated in the perinatal (late fetal or neonatal) period died of cancers prior to 2 years of age. This risk was of significant increase compared to the risks for other experimental groups and for the canine population in general. Overall, 71% (5 of 7) of all cancers and 56% (10 of 18) of all benign and malignant neoplasms seen in the first 4 years of life occurred in 29% (480 of 1,680) of the dogs irradiated in the perinatal period. These data suggest an increased risk for neoplasia after perinatal irradiation in dogs.

Hexokinase I is a Gli2-responsive gene expressed in the embryonic CNS.

Little is known about the downstream genes regulated by Gli zinc finger transcription factors, which are targets and mediators of Hedgehog signaling. Specifically, the identity and regulation of genes which mediate Gli2 function in neurogenesis are unclear. We describe here the cloning of frog Hexokinase I (HKI) as a Gli2-responsive gene. We show that HKI expression is induced by Gli2 and that it is detected in defined neuronal populations. Since the primary energy source of the brain is derived from glucose metabolism and hexokinase catalyses the first and rate limiting step in this process, the conversion of glucose into glucose-6-phosphate, these findings suggest a link between the regulation of neuronal induction and differentiation.

The selector gene cut represses a neural cell fate that is specified independently of the Achaete-Scute-Complex and atonal.

The peripheral nervous system (PNS) of Drosophila offers a powerful system to precisely identify individual cells and dissect their genetic pathways of development. The mode of specification of a subset of larval PNS cells, the multiple dendritic (md) neurons (or type II neurons), is complex and still poorly understood. Within the dorsal thoracic and abdominal segments, two md neurons, dbd and dda1, apparently require the proneural gene amos but not atonal (ato) or Achaete-Scute-Complex (ASC) genes. ASC normally acts via the neural selector gene cut to specify appropriate sensory organ identities. Here, we show that dbd- and dda1-type differentiation is suppressed by cut in dorsal ASC-dependent md neurons. Thus, cut is not only required to promote an ASC-dependent mode of differentiation, but also represses an ASC- and ato-independent fate that leads to dbd and dda1 differentiation.

Analyses of heat transfer in stationary and rotating ribbed blade cooling passages using computational fluid dynamics.

Computational fluid dynamics (CFD) predictions of the flow patterns and heat transfer in simplified ribbed-wall turbine blade cooling passages were performed for representative stationary and rotating conditions. Analyses have been performed with different mesh densities and using different turbulence models to assess the sensitivity of predictions to these variables. Computed local heat transfer results are compared to measurements available in the literature to assess their accuracy. The results generally agree well with experiment, although the peak values of the heat transfer coefficients were under-predicted in the first leg of the channel. Some sensitivity to mesh density was seen, while the choice of near-wall turbulence model appeared to have little effect.

Conversion of the arthrodesed hip to a total hip arthroplasty.

Total hip arthroplasty was done in thirty-three patients who had had previous surgical attempts at arthrodesis of the hip. The arthrodesis had failed in nineteen patients, and the other fourteen patients had fused hips with symptoms in the knee and lower back. Thirty-one of the patients had satisfactory functional ability after total hip arthroplasty after one to three and one-half years' follow-up. The two patients in whom the procedure failed had complicating infections.

Extra-abdominal desmoid tumors.

One hundred and ninety-four patients with extra-abdominal desmoid tumors, most of them in the extremities, have been treated at the Mayo Clinic. One hundred and thirty-two patients (68 per cent) experienced a recurrence at an average of 1.4 years after the first treatment. A greater tendency for recurrence was evident in female patients, in patients who were more than thirty years old, in certain anatomical locations (especially the foot and calf), and most importantly after treatment by intralesional or marginal excision. In view of the excellent prognosis for survival, we recommend wide local excision when anatomically feasible or marginal excision and postoperative radiation therapy when function of the extremity would be severely compromised if excision with wide margins were done. A recurrent lesion that does not appear to be growing should be followed until evidence of growth of the lesion precipitates a secondary wide excision.

Relationship of hypothyroidism to diabetes mellitus, renal amyloidosis, and thrombosis in purebred beagles.

Review of 484 records for colony Beagles revealed an association between hypothyroidism and diabetes mellitus. The average time between first notation of hypothyroidism and later development of diabetes mellitus was 2.8 years. An association was also made with hypothyroidism, renal amyloidosis, and thrombosis. Hypothyroidism was significantly related to thrombosis, thrombosis was significantly related to renal amyloidosis, but hypothyroidism and renal amyloidosis were not significantly related. Of 62 hypothyroid dogs, 11 were diabetic and 7 others had thrombosis. Six hypothyroid dogs had renal amyloidosis, 4 of which had thrombosis. One dog had renal amyloidosis and thrombosis in the absence of hypothyroidism. There does not appear to be an association with any of the lesions and previous low-dose, whole-body gamma, or sham irradiation.

Continuous warm blood cardioplegia: a new technique for myocardial protection.

Hypothermia is used to prolong the safe period of ischemic arrest by reducing the heart's oxygen demands. Due to this effect, hypothermia has been the fundamental component of most methods of myocardial protection during cardiac surgery. However, hypothermia has a number of unwanted side effects, such as detrimental effects on enzyme function, energy generation, and cell membranes. Since electromechanical arrest accounts for 90% of myocardial oxygen consumption, arresting the heart with chemical cardioplegia will reduce O2 consumption dramatically. Therefore, if the resting (arrested) heart is continuously perfused with oxygenated blood cardioplegia, one can easily provide the remaining 10% of O2 that it requires. Under these conditions, the need for hypothermia becomes questionable. In this paper, we describe the perfusionist's experience using the antegrade and retrograde technique of continuous warm blood cardioplegia.

Self assembly modulated by interactions of two heterogeneously charged surfaces.

Recent experiments have measured attractive interactions between two surfaces that each bear two molecular species with opposite charge. Such surfaces form charged domains of finite size. We present a theoretical model that predicts the dependence of the domain size, phase behavior and the interlayer forces as a function of spacing and salt concentration for two such interacting surfaces. A strong correlation between two length scales, the screening length and the surface separation, at the spinodal is shown. Remarkably, the first-order phase transition to infinite sized domains depends logarithmically on the ratio of the domain size to the molecular size. Finally, we fit the predicted pressure with experiments.

Synthesis of a peptidocalix[4]arene library and identification of compounds with hydrolytic activity.

A 120 member library of peptidocalix[4]arenes was synthesized and screened for catalysis of the hydrolysis of p-nitrophenyl acetate. His-Ser-His-calix[4]arene was found to catalyze this reaction with v(0)=3.24 x 10(-8)M/s, an increase of 1520% above background and 30% above the tripeptide (His-Ser-His) alone.

Getting a-head of the organizer: anterior-posterior patterning of the forebrain.

The molecular mechanisms that drive the development of embryonic tissues are being uncovered rapidly. One such fascinating example is the development of the forebrain, the most anterior part of the nervous system. In this review, we will discuss the mechanisms that induce the formation of the forebrain in multiple vertebrate systems, placing emphasis on a recent article published by Grinblat et al. ((1)) Using zebrafish as a model system, these authors combine elegant embryological manipulations with the use of early markers of the presumptive forebrain, to show that initial induction and patterning of this tissue occurs near the onset of gastrulation. In addition, their results confirm observations made in other systems that planar signals, those traveling in the plane of the ectoderm, are involved in forebrain induction and patterning.

Origin and specification of type II sensory neurons in Drosophila.

The peripheral nervous system (PNS) of Drosophila is a preferred model for studying the genetic basis of neurogenesis because its simple and stereotyped pattern makes it ideal for mutant analysis. Type I sensory organs, the external (bristle-type) sensory organs (es) and the internal (stretch-receptive) chordotonal organs (ch), have been postulated to derive from individual ectodermal precursor cells that undergo a stereotyped pattern of cell division. Little is known about the origin and specification of type II sensory neurons, the multiple dendritic (md) neurons. Using the flp/FRT recombinase system from yeast, we have determined that a subset of md neurons derives from es organ lineages, another subset derives from ch organ lineages and a third subset is unrelated to sensory organs. We also provide evidence that the genes, numb and cut, are both required for the proper differentiation of md neurons.

Cell lineage analysis of the Drosophila peripheral nervous system.

The peripheral nervous system (PNS) of Drosophila provides a very well-characterized model system for studying the genes involved in basic processes of neurogenesis. Because of its simplicity and stereotyped pattern, each cell of the PNS can be individually identified and the phenotypic consequences of mutations can be studied in detail. Thus, some of the genetic mechanisms leading to the formation of type I sensory organs, the external, bristle-type sensory organs (es), and the internal, stretch-receptive chordotonal organs (ch) have been elucidated. Each sensory organ seems to be generated by a stereotyped pattern of cell division of individual ectodermal precursor cells. Recent advances in cell lineage analysis of the PNS have provided a detailed picture of almost all the lineages in the PNS, including those giving rise to the type II sensory neurons, also known as multiple dendritic (md) neurons. This knowledge will be instrumental in the precise characterization of the phenotypes associated with mutations in known and new genes and their interactions which determine cell fate decisions during neurogenesis. Here, we describe and compare three recently developed methods by which cell lineages have been assessed: single cell transplantation, bromodeoxyuridine (BrdU) incorporation studies, and the flp/FRT recombinase system from yeast. In the light of a more complete knowledge of the PNS lineages, we will discuss the effects of known mutations that alter neuronal cell fates.