A Unifying Framework for Understanding Biological Structures and Functions Across Levels of Biological Organization

The relationship between structure and function is a major constituent of the rules of life. Structures and functions occur across all levels of biological organization. Current efforts to integrate conceptual frameworks and approaches to address new and old questions promise to allow a more holistic and robust understanding of how different biological functions are achieved across levels of biological organization. Here, we provide unifying and generalizable definitions of both structure and function that can be applied across all levels of biological organization. However, we find differences in the nature of structures at the organismal level and below as compared to above the level of the organism. We term these intrinsic and emergent structures, respectively. Intrinsic structures are directly under selection, contributing to the overall performance (fitness) of the individual organism. Emergent structures involve interactions among aggregations of organisms and are not directly under selection. Given this distinction, we argue that while the functions of many intrinsic structures remain unknown, functions of emergent structures are the result of the aggregate of processes of individual organisms. We then provide a detailed and unified framework of the structure-function relationship for intrinsic structures to explore how their unknown functions can be defined. We provide examples of how these scalable definitions applied to intrinsic structures provide a framework to address questions on structure-function relationships that can be approached simultaneously from all subdisciplines of biology. We propose that this will produce a more holistic and robust understanding of how different biological functions are achieved across levels of biological organization.

Correction: A study of the depth and size of concave cube Au nanoparticles as highly sensitive SERS probes

Correction for 'A study of the depth and size of concave cube Au nanoparticles as highly sensitive SERS probes' by J. M. Romo-Herrera et al., Nanoscale, 2016, 8, 7326-7333.

A study of the depth and size of concave cube Au nanoparticles as highly sensitive SERS probes

High and uniform near fields are localized at the eight similar sharp corners of cubic gold nanoparticles. Moreover, by introducing concavity in the particle lateral planes, such field intensities can be further increased and tuned in the near infrared region without altering the overall size of the nanoparticles. Herein, we perform a thorough investigation of the morphological, crystallographic and plasmonic properties of concave gold nanocubes (GNCs) in the sub-70 nm size range, for their potential application as highly efficient SERS substrates in size-limiting cases. Theoretical calculations indicate that the highest increment of the near-field is located at the eight sharp tips and, interestingly, a medium near-field increment is also activated over the volume next to the concave surface. Remarkably, the plasmonic response of the concave cubic morphology showed great sensitivity to the concavity degree. Experimental SERS analysis nicely matches the outcome of the theoretical model, confirming that medium-sized concave GNCs (35 nm side length) possess the highest SERS activity upon excitation with a 633 nm laser, whereas larger 61 nm side concave GNCs dominate the optical response at 785 nm. Due to their size-intensity trade off, we envision that such small concave gold nanocubes can provide a highly active and efficient SERS platform for size-limiting applications, especially when near infrared excitations are required.

A charge-dipole interaction model for the frequency-dependent polarizability of silver clusters

We present a charge-dipole interaction model for the calculation of the frequency-dependent polarizability of silver clusters. The model relies on the representation of silver atoms by both a net electric charge and a dipole. Time variations of the atomic charges are related to the currents that flow through the bonds of the structures considered and the atomic charges and dipoles are eventually determined from the application of a least-action principle. After a generalization that enables the bonds of the bulk and surface atoms to have specific resistances, the model is parameterized on data obtained by the time-dependent density functional theory for tetrahedral Ag(20), Ag(84) and Ag(120) clusters. We then study the polarization properties of dimers of silver clusters. We compare in particular the polarizability of the dimers with that of the isolated clusters, for a range of gap distances and frequencies. We also consider the field enhancements one can achieve with these systems. The results are in good agreement with reference data and enable an extension of these data to a wider range of situations. They show that significant field enhancements are achieved at frequencies associated with resonant polarization along the axis of the dimer.

Occupation and small bowel adenocarcinoma: a European case-control study

OBJECTIVES

Because of the rarity of small bowel adenocarcinoma (SBA), little is known about the aetiology of this disease. This study aimed to identify occupational clustering of cases SBA as a systematic approach to new hypotheses on the aetiology of this disease.

METHODS

A European multicentre case-control study was conducted in 1995-7, inclusive. Incident cases aged 35-69 years with SBA (n=168) were recruited before acceptance by a pathologist. Altogether 107 cases and 3915 controls were accepted, of which 79 cases, 579 colon cancer controls, and 2070 population controls were interviewed.

RESULTS

The strongest industrial risk factors for SBA taking account of 10 years' exposure lag were dry cleaning, manufacture of workwear, mixed farming (women), and manufacture of motor vehicles (men). A significantly increased risk of SBA (odds ratio (OR) and 95% confidence interval (95% CI)) was found among men employed as building caretakers, OR 6.7 (1.7 to 26.0) and women employed as housekeepers, OR 2.2 (1.1 to 4.9); general farm labourers, OR 4.7 (1.8 to 12.2); dockers, OR 2.9 (1.0 to 8.2); dry cleaners or launderers, OR 4.1 (1.2 to 13.6); and textile workers (sewers or embroiderers), OR 2.6 (1.0 to 6.8). For the last four groups, together with welders OR 2.7 (1.1 to 6.6) (men) an exposure-response pattern was found when calculating the ORs for jobs held 1-5 years and >5 years, with never having held the job as reference. The ORs (95% CIs) for 1-5 years and >5 years were 4.3 (0.4 to 44.0) and 3.5 (0.9 to 13.7), 3.0 (0.3 to 26.2) and 4.3 (0.9 to 21.2), 4.6 (0.4 to 48.1) and 11.0 (2.0 to 60.4), 1.3 (0.2 to 11.0) and 5.8 (2.0 to 17.2), and 2.8 (0.3 to 23.8) and 4.6 (1.3 to 16.6), respectively, for each of these occupations. Among welders, people performing semiautomatic arc welding (MIG/MAG) were identified as a high risk group (OR 5.0 (1.3 to 19.6)).

CONCLUSIONS

This explorative study suggests an increased occurrence of SBA in certain occupations, which needs further evaluation.

[Risk factors for preeclampsia. Multivariate analysis]

OBJECTIVE

To determine in multivariate analysis the clinical, social, and demographic factors for preeclampsia.

STUDY DESIGN

A case-control study was designed. Three hundred patients were included, divided in two groups. 150 cases with criteria diagnosis for preeclampsia. 150 patients with normal pregnancy and deliveries. The main variables analyzed were age, schooling, marital status, employment, socioeconomic status, smoking and alcohol consumption, body mass index, familiar history of preeclampsia, history of preeclampsia in previous pregnancy, parity and type of pregnancy (single or multiple).

STATISTICAL ANALYSIS

For comparison of cases and controls on categorical variables, odds ratios and 95% confidence intervals were calculated, and multiple logistic regression analyses.

RESULTS

Multiple logistic regression analysis showed that history of preeclampsia in previous pregnancy has OR 23.7, 95% p < 0.001, familiar history of preeclampsia OR 1.62, p < 0.08, high body mass has OR 1.60.

CONCLUSIONS

The knowledge of the most important risk factors in our population could be useful for the clinical to pre-detect the patient who will develop preeclampsia.

[Long-term course of liver rupture in preeclampsia. A case report]

A case report is presented of one preeclamptic patient with rupture of a big right subcapsular hematoma of the liver which was misdiagnosed with cholecystitis. A cesarean delivery was performed, which resulted is stillbirth, with abruptio placentae of 50%. The emergent treatment of the liver rupture was the right hepatic artery ligation, the postoperative development was favorable. Long term follow-up using ultrasound and liver function values were performed for 14 months and showed that the lesion has regressed with a normal hepatic imaging.

Socioeconomic risk factors in the prevalence of asthma and other atopic diseases in children 6 to 7 years old in Valencia Spain

A cross-sectional survey of a cohort study was carried out between June and December 1994 in Valencia, Spain (population in 1994: 764,293 inhabitants). Two hundred sixty public and private schools randomly selected from the total of schools in Valencia were invited to participate; 3948 children aged 6-7 years cooperated in our study after informed consent was obtained from parents and school director. The survey in Valencia is part of the International Study of Asthma and Allergy in Childhood (ISAAC). Prevalences for asthma, rhinitis and atopic dermatitis were determined and contrasted with socioeconomic status (SES) among children. No statistically significant associations were established between the prevalences of asthma, rhinitis and atopic dermatitis, and SES. However, atopic dermatitis was found to be common among upper class children (21.5 per 100 children). Likewise, significant associations were observed between the severity of atopy (2 or 3 atopic manifestations) and SES (p = 0.000), being greater for lower strata (4.5 per 100 children); for the three SES level significant differences were established (p = 0.008) regarding passive exposure to tobacco smoke in the home.

Co-evolution of rat TAP transporters and MHC class I RT1-A molecules

The genes for rat major histocompatibility complex (MHC) class I molecules are associated either with those for the A allele of the transporter associated with antigen processing (TAP-A), which can transport peptides with basic carboxy-terminal residues, or with those for TAP-B, which cannot [1-5]. To explore whether these associations have a functional basis, we compared the sequences of 13 rat MHC class la RT1-A cDNAs from nine MHC haplotypes. Of seven TAP-A- linked RT1-A molecules, six possess strongly acidic F pockets, and these bind a high proportion of peptides with basic carboxy-terminal residues. The F pockets of TAP-B-linked molecules, by contrast, were more basic. Furthermore, we identified six positions at the 'righthand end' of the peptide-binding groove, at which a majority of TAP-B-linked molecules diverge from the consensus sequence for class la molecules whereas, at these positions, all the TAP-A-linked molecules reflect the consensus sequence. Our results suggest that the linked rat class la and TAP genes have co-evolved to maximize the supply of appropriate peptides to the presenting molecules.

Treatment with anti-LFA-1 alpha monoclonal antibody selectively interferes with the maturation of CD4- 8+ thymocytes

Maturation of T lymphocytes in the thymus is driven by signals provided by soluble factors and by the direct interaction between thymocytes and stromal cells. Although the interaction between T-cell receptor (TCR) and major histocompalibility complex (MHC) molecules on stromal cells is crucial for T-cell development, other accessory molecules seem to play a role in this process. In order to better understand the role of lymphocyte function-associated antigen-1 (LFA-1) and intercellular adhesion molecule-1 (ICAM-1) molecules in thymocyte maturation, mice were treated from birth with saturating doses of non-cytolytic-specific monoclonal antibodies. The effect of this treatment on thymocyte subpopulations and the expression of CD3 and TCR-alpha beta by these cells was investigated by flow cytometry. Our data demonstrated that the effective saturation of LFA-1 alpha chain in the thymus, but not ICAM-I or LFA-I beta chain, selectively interfered with the maturation of CD8+ T cells, as manifested by a marked reduction in the frequency of CD4-8+ thymocytes expressing high levels of CD3 and TCR-alpha beta. This selective reduction was also observed in peripheral blood mononuclear cells and spleen cells. The analysis of the frequencies of various V beta TCR showed that CD4-8+ thymocytes were globally affected by the treatment. These results underline the importance of the interaction between LFA-1 and its ligands in the maturation of CD8+ T cells and document the existence of different molecular requirements for the differentiation of CD4+ and CD8+ T cells.

The ability of B cells to participate in allogeneic cognate T-B cell interactions in vitro depends on the presence of CD4+ T cells during their development

We have assessed in vitro whether the absence of T cells in the natural environment of F1 hybrid mice influences the ability of their B cells to participate in an allogeneic interaction with CD4+ cells from parental mice. For this purpose, B cells from athymic CB6F1 nu/nu mice or from CB6F1 mice depleted in different T cell subsets were incubated in vitro with purified CD4+ BALB/c cells. Here, we show that B cells from CB6F1 nu/nu mice or from euthymic CB6F1 mice depleted from birth of CD4+ cells were unable to respond to allogeneic stimulation with BALB/c CD4+ T cells, which produce normal levels of cytokines. The addition of dendritic cells from euthymic CB6F1 mice did not revert this defect. B cells from CB6F1 mice lacking CD4+ T cells showed a selective reduction in the expression of CD23. We found a complete restoration of both the CD23 expression and the ability of CB6F1 nu/nu B cells to respond in vitro to an allogeneic stimulation by CD4+ cells in two instances: (1) after neonatal engraftment of a syngeneic thymus into CB6F1 nu/nu mice, which partially reconstitutes the mature T cell populations; and (2) after preincubation of B cells from CB6F1 nu/nu mice with high concentrations of rIL-4. However, the addition of an anti-CD23 mAb did not interfere with the polyclonal activation of CB6F1 B cells in this system. These results indicate that CD4+ cells play an important role in the functional maturation of B cells by promoting their ability to participate in allogeneic cognate T-B cell interactions.

The ability of B cells to participate in allogeneic cognate T-B cell interactions in vitro depends on the presence of CD4+ T cells during their development

We have assessed in vitro whether the absence of T cells in the natural environment of F1 hybrid mice influences the ability of their B cells to participate in an allogeneic interaction with CD4+ cells from parental mice. For this purpose, B cells from athymic CB6F1 nu/nu mice or from CB6F1 mice depleted in different T cell subsets were incubated in vitro with purified CD4+ BALB/c cells. Here, we show that B cells from CB6F1 nu/nu mice or from euthymic CB6F1 mice depleted from birth of CD4+ cells were unable to respond to allogeneic stimulation with BALB/c CD4+ T cells, which produce normal levels of cytokines. The addition of dendritic cells from euthymic CB6F1 mice did not revert this defect. B cells from CB6F1 mice lacking CD4+ T cells showed a selective reduction in the expression of CD23. We found a complete restoration of both the CD23 expression and the ability of CB6F1 nu/nu B cells to respond in vitro to an allogeneic stimulation by CD4+ cells in two instances: (1) after neonatal engraftment of a syngeneic thymus into CB6F1 nu/nu mice, which partially reconstitutes the mature T cell populations; and (2) after preincubation of B cells from CB6F1 nu/nu mice with high concentrations of rIL-4. However, the addition of an anti-CD23 mAb did not interfere with the polyclonal activation of CB6F1 B cells in this system. These results indicate that CD4+ cells play an important role in the functional maturation of B cells by promoting their ability to participate in allogeneic cognate T-B cell interactions.