Change of waveform in bacterial flagella: The role of mechanics at the molecular level

The flagella of Salmonella and other bacteria are constructed from molecules of the protein flagellin in a way which permits relatively easy transition between members of a family of distinct stable left and right-handed helical waveforms. Changes of waveform, particularly between “normal” (left-handed) and “curly” (right-handed) play an important role in the switch from smooth swimming to tumbling in chemotaxis. This paper establishes some mechanical properties of model flagella built from bi-stable subunits, which in turn clarifies the mechanics of the changes of waveform which occur, in a viscous fluid environment, at various points in the swimming cycle.Available data on the joining of different helical waveforms in a single filament, supplemented by information on the way in which helical filaments flatten down in preparation for electron microscopy, are well-fitted by the mechanical behaviour of an assembly of mechanical subunits having some simple distinctive design features. The same arrangement makes possible an explanation for the formation of flagellar-like but straight polymers from Salmonella flagellin in the presence of high concentrations of NaCl.     

New insights on the role of apoptosis and autophagy in HIV pathogenesis

Viruses manipulate host cells to ensure their own survival and, at late stages of the viral life cycle, they kill the infected target cell to ensure their propagation. In addition, some viruses induce a bystander killing, a viral strategy to escape from the host's innate and cognate defense systems. In HIV-infection, the disabling of the immune system is initially due to the preferential depletion by apoptosis of virus-specific CD4⁺ T cells in lymphoid tissues, followed by the destruction of non-infected bystander cells. Both the extrinsic and the intrinsic pathways are activated, and this is the consequence of systemic immune activation. This review presents recent developments showing that the gastrointestinal tract is the major reservoir of infected cells and the site of rapid and profound loss of CD4 T cells, and that microbial translocation from the gastrointestinal tract is the cause of immune activation. Furthermore, apoptosis mechanisms involved in HIV-induced neuropathological disorders are discussed, including the role of syncytia that involve the sequential activation of ATM, p38MAPK and p53. Finally, HIV-associated dementia (HAD) was recently found in monkey models to be linked to inhibition of autophagy in neurons, suggesting that homeostasis of autophagy is a reliable security factor for neurons, and challenging the development of new therapeutics aimed at boosting neuronal autophagy to prevent HAD.     

History of Protein Data Bank Japan: standing at the beginning of the age of structural genomics

Prof. Haruki Nakamura, who is the former head of Protein Data Bank Japan (PDBj) and an expert in computational biology, retired from Osaka University at the end of March 2018. He founded PDBj at the Institute for Protein Research, together with other faculty members, researchers, engineers, and annotators in 2000, and subsequently established the worldwide Protein Data Bank (wwPDB) in 2003 to manage the core archive of the Protein Data Bank (PDB), collaborating with RCSB-PDB in the USA and PDBe in Europe. As the former head of PDBj and also an expert in structural bioinformatics, he has grown PDBj to become a well-known data center within the structural biology community and developed several related databases, tools and integrated with new technologies, such as the semantic web, as primary services offered by PDBj.     

The integral role of the plastic surgeon at a level I trauma center

The role of plastic surgery in urban level I trauma centers in the United States has been largely undefined, despite the undeniable historical involvement of plastic surgery in reconstruction of posttraumatic defects. To explore and define this role, case data were prospectively collected during a 29-month period following initiation of a full-time plastic surgery position at an established urban level I trauma center. Referring and/or interacting surgical service, anatomical area of interest, and procedure data were tabulated. A total of 1009 operative reports comprising 1104 procedures were recorded. The most common interacting surgical services were orthopedics and general/trauma surgery; however, interaction occurred with a total of 10 surgical specialties. The upper extremity was the most common anatomical area operated on followed by head and neck, lower extremity, trunk, urogenital, and breast. A wide variety of procedures were performed in each anatomical area, demonstrating the broad scope of reconstructive surgery practiced in a trauma setting. Three hundred and twenty-four procedures involved expertise in microsurgery, flaps, and burn or frostbite care. Additional procedures commonly performed demonstrated considerable overlap with other fields of surgical specialization. This overlap in skills proved advantageous in distribution of facial trauma call and hand surgery coverage. Data presented in this study reinforce the idea that plastic surgery is a specialty defined by concept rather than anatomical area, and also demonstrate a significant role for plastic surgeons in a level I trauma center.     

The use of genetic tools for the evaluation of a potential migration barrier for the bullhead

Microsatellite analysis and computer simulations strongly suggested that a culvert, i.e . a connection between two river stretches by a narrow tube underneath an artificial channel, was not a migration barrier for the endangered bullhead Cottus gobio .     

The reactions of plant hormones with reactive oxygen species: chemical insights at a molecular level

The reactions of two plant hormones, namely jasmonic acid (JA) and methyl jasmonate (MJ), with different reactive oxygen species (ROS) were investigated using the density functional theory. Different reaction sites and mechanisms were explored, as well as solvents of different polarity, and pH in aqueous solution. The thermochemical viability and kinetics of the investigated reaction pathways were found to be strongly influenced by the reacting ROS. All the investigated pathways were found to be exergonic, both in aqueous and lipid solution and for both JA and MJ, when the reactions involve ^?OH and ^?OCH₃. On the contrary, for the reactions with peroxy radicals (^?OOH and ^?OOCH₂CHCH₂) only a few hydrogen transfer pathways were found to be thermochemically viable. The reactions involving ^?OH were found to be diffusion-controlled, with both JA and MJ, regardless of the polarity of the solvent. This led to the hypothesis that the direct ^?OH scavenging activity of JA and MJ might play a role in the beneficial effects of the jasmonate family regarding the antioxidant defense of plants against metal-induced oxidative stress. The deprotonated fraction of JA is, to some extent, more reactive than the neutral fraction toward ROS. This, together with the acid-base equilibria inherent to some ROS, make the pH an influential environmental factor on the overall reactivity of JA toward ROS.     

Comparative investigations of manual action representations: evidence that chimpanzees represent the costs of potential future actions involving tools

The ability to adjust one's ongoing actions in the anticipation of forthcoming task demands is considered as strong evidence for the existence of internal action representations. Studies of action selection in tool use reveal that the behaviours that we choose in the present moment differ depending on what we intend to do next. Further, they point to a specialized role for mechanisms within the human cerebellum and dominant left cerebral hemisphere in representing the likely sensory costs of intended future actions. Recently, the question of whether similar mechanisms exist in other primates has received growing, but still limited, attention. Here, we present data that bear on this issue from a species that is a natural user of tools, our nearest living relative, the chimpanzee. In experiment 1, a subset of chimpanzees showed a non-significant tendency for their grip preferences to be affected by anticipation of the demands associated with bringing a tool's baited end to their mouths. In experiment 2, chimpanzees' initial grip preferences were consistently affected by anticipation of the forthcoming movements in a task that involves using a tool to extract a food reward. The partial discrepancy between the results of these two studies is attributed to the ability to accurately represent differences between the motor costs associated with executing the two response alternatives available within each task. These findings suggest that chimpanzees are capable of accurately representing the costs of intended future actions, and using those predictions to select movements in the present even in the context of externally directed tool use.     

Crystal polymorphism of pharmaceuticals: probing crystal nucleation at the molecular level

Paracetamol, sulfathiazole and l-glutamic acid are presented as examples of pharmaceutical crystal polymorphic systems. The effect of N-acylated sulfathiazole derivatives (3–6) on sulfathiazole crystallisation is discussed, and possible modes of action presented. Methods for the control of the crystal polymorphism of l-glutamic acid which utilise the principles of conformation mimicry and co-operative binding are presented. The preparation of a series of bis-amides of EDTA derived from sulfathiazole, 5-aminoisophthalic acid and 4-hydroxyaniline (i.e. compounds 9a–c) is presented, as is data on the effect of these compounds on the crystallisation of, respectively, sulfathiazole, l-glutamic acid and paracetamol.     

The conformational feasibility for the formation of reaching dimer in ASV and HIV integrase: a molecular dynamics study

Retroviral integrases are reported to form alternate dimer assemblies like the core–core dimer and reaching dimer. The core–core dimer is stabilized predominantly by an extensive interface between two catalytic core domains. The reaching dimer is stabilized by N-terminal domains that reach to form intermolecular interfaces with the other subunit’s core and C-terminal domains (CTD), as well as CTD–CTD interactions. In this study, molecular dynamics (MD), Brownian dynamics (BD) simulations, and free energy analyses, were performed to elucidate determinants for the stability of the reaching dimer forms of full-length Avian Sarcoma Virus (ASV) and Human Immunodeficiency Virus (HIV) IN, and to examine the role of the C-tails (the last ~16–18 residues at the C-termini) in their structural dynamics. The dynamics of an HIV reaching dimer derived from small angle X-ray scattering and protein crosslinking data, was compared with the dynamics of a core–core dimer model derived from combining the crystal structures of two-domain fragments. The results showed that the core domains in the ASV reaching dimer express free dynamics, whereas those in the HIV reaching dimer are highly stable. BD simulations suggest a higher rate of association for the HIV core–core dimer than the reaching dimer. The predicted stability of these dimers was therefore ranked in the following order: ASV reaching dimer < HIV reaching dimer < composite core–core dimer. Analyses of MD trajectories have suggested residues that are critical for intermolecular contacts in each reaching dimer. Tests of these predictions and insights gained from these analyses could reveal a potential pathway for the association and dissociation of full-length IN multimers.     

The strain-generated electrical potential in cartilaginous tissues: a role for piezoelectricity

The strain-generated potential (SGP) is a well-established mechanism in cartilaginous tissues whereby mechanical forces generate electrical potentials. In articular cartilage (AC) and the intervertebral disc (IVD), studies on the SGP have focused on fluid- and ionic-driven effects, namely Donnan, diffusion and streaming potentials. However, recent evidence has indicated a direct coupling between strain and electrical potential. Piezoelectricity is one such mechanism whereby deformation of most biological structures, like collagen, can directly generate an electrical potential. In this review, the SGP in AC and the IVD will be revisited in light of piezoelectricity and mechanotransduction. While the evidence base for physiologically significant piezoelectric responses in tissue is lacking, difficulties in quantifying the physiological response and imperfect measurement techniques may have underestimated the property. Hindering our understanding of the SGP further, numerical models to-date have negated ferroelectric effects in the SGP and have utilised classic Donnan theory that, as evidence argues, may be oversimplified. Moreover, changes in the SGP with degeneration due to an altered extracellular matrix (ECM) indicate that the significance of ionic-driven mechanisms may diminish relative to the piezoelectric response. The SGP, and these mechanisms behind it, are finally discussed in relation to the cell response.     

The role of glycine residues at the C-terminal peptide segment in antinociceptive activity: a molecular dynamics simulation

Elucidating structural determinants in the functional regions of toxins can provide useful knowledge for designing novel analgesic peptides. Glycine residues at the C-terminal region of the neurotoxin BmK AGP-SYPU2 from the scorpion Buthus martensii Karsch (BmK) have been shown to be crucial to its analgesic activity. However, there has been no research on the structure–function relationship between the C-terminal segment of this toxin and its analgesic activity. To address this issue, we performed three MD simulations: one on the native structure and the other two on mutants of that structure. Results of these calculations suggest that the existence of glycine residues at the C-terminal segment stabilizes the protruding topology of the NC domain, which is considered an important determinant of the analgesic activity of BmK AGP-SYPU2.     

The rising level of medical student debt: potential risk for a national default

At the turn of the 20th century, mostly as a result of the Flexner report, medical education changed dramatically by establishing a scientific basis for the study of medicine within the institutions of the major universities. There have been major and dramatic changes in medicine during the past 80 years that have improved medical education in the United States, but these changes have also placed major economic strains on students who have educational debts. If medicine is a social responsibility to the public, then the public should share the responsibility of identifying and supporting new approaches to funding and financially managing the teaching of future physicians. There is no universal solution because there are various approaches institutions may take to structure these financial responsibilities. This article describes trends in medical student educational debt, identifies the financial needs of medical students, and proposes ways of addressing those needs to avert a possible national financial crisis among medical students. We must invest in medical students because they will be the leaders we need to help care for our society and our own families in the next century.     

Geographic variation in adaptation at the molecular level: a case study of plant immunity genes

Natural selection imposed by interacting species frequently varies among geographic locations and can lead to local adaptation, where alternative phenotypes are found in different populations. Little is known, however, about whether geographically variable selection acting on traits that mediate species interactions is consistent or strong enough to influence patterns of nucleotide variation at individual loci. To investigate this question, we examined patterns of nucleotide diversity and population structure at 16 plant innate immunity genes, with putative functions in defending plants against pathogens or herbivores, from six populations of teosinte (Zea mays ssp. parviglumis). Specifically, we tested whether patterns of population structure and within-population diversity at immunity genes differed from patterns found at nonimmunity (reference) loci and from neutral expectations derived from coalescent simulations of structured populations. For the majority of genes, we detected no strong evidence of geographically variable selection. However, in the wound-induced serine protease inhibitor (wip1), which inhibits the hydrolysis of dietary proteins in insect herbivores, one population showed unusually high levels of genetic differentiation, very low levels of nucleotide polymorphism, and was fixed for a novel replacement substitution in the active site of the protein. Taken together, these data suggest that wip1 experienced a recent selective sweep in one geographic region; this pattern may reflect local adaptation or an ongoing species-wide sweep. Overall, our results indicate that a signature of local adaptation at the molecular level may be uncommon-particularly for traits that are under complex genetic control.     

Increased plasma levels of extracellular mitochondrial DNA during HIV infection: a new role for mitochondrial damage-associated molecular patterns during inflammation

HIV infection is characterized by a chronic inflammatory state. Recently, it has been shown that mitochondrial DNA (mtDNA) released from damaged or dead cells can bind Toll like receptor-9 (TLR9), an intracellular receptor that responds to bacterial or viral DNA molecules. The activation of TLR9 present within monocytes or neutrophils results in a potent inflammatory reaction, with the production of proinflammatory cytokines. We measured plasma levels of mtDNA in different groups of HIV⁺ patients, i.e., those experiencing an acute HIV infection (AHI), long term non progressors (LTNP), late presenters (LP) taking antiretroviral therapy for the first time, and healthy controls. We found that in AHI and LP mtDNA plasma levels were significantly higher than in healthy individuals or in LTNP. Plasma mtDNA levels were not correlated to peripheral blood CD4⁺ T cell count, nor to markers of immune activation, but had a significant correlation with plasma viral load, revealing a possible role for mtDNA in inflammation, or as a biomarker of virus-induced damage.     

Methylfolate modulates potassium evoked neuro-secretion: Evidence for a role at the pteridine cofactor level of tyrosine 3-hydroxylase

We have previously shown that 5-methyltetrahydrofolate influences neuro-secretion. The present study more precisely characterises the processes involved and considers one probable site of action. Focusing on the tyrosine-noradrenalin axis in cerebellum we showed 5-methyltetrahydrofolate causes a significant reduction in the apparent K⁺ evoked secretion of noradrenalin to only 12.9% of control release. Evidence supports the idea that this could actually be due to increased synthesis leading to; depletion of reserves, possibly through leakage, exocytotic inhibition via activation of presynaptic receptors or end product inhibition by noradrenalin at the pteridine cofactor level of tyrosine hydroxylase: a) concomitant decreased measurement of perfusate and intracellular tyrosine with released noradrenalin following 5-methyltetrahydrofolate treatment supports the idea of increased transmitter turn over; b) kinetic studies indicate that at saturating concentrations of tyrosine and in the presence of an inhibitor of L-DOPA decarboxylase, 5-methyltetrahydrofolate partially duplicates the rate limiting behaviour of a synthetic pteridine cofactor — DL,2-amino-4-hydroxy-6,7,dimethyltetrahydropteridine. We debate whether, in vivo, CSF 5-methyltetrahydrofolate might interact at the tetrahydrobiopterin cofactor level of tyrosine hydroxylase and other aromatic amino-acid hydroxylases.     

The use of the electrostatic potential at the molecular surface in recognition interactions: Dibenzo-p-dioxinsand related systems

An ab initio self-consistent-field molecular orbital approach was used to compute the electrostatic potentials of dibenzo-p-dioxin, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), two analogues of the latter, and two isomeric benzoflavones on a three-dimensional molecular surface corresponding to the contour of constant electronic density equal to 0.002 electrons/bohr³. The results are discussed in relation to the biological activities of the respective molecules. It is shown that the electrostatic potential graphically depicted on the molecular surface is well suited for the study of recognition interactions, such as are believed to be involved in the initial receptor-mediated step leading to toxicity in the dibenzo-p-dioxins. The surface potential has the advantage of clearly showing steric features that may play a role in understanding the recognition process being investigated.     

Single-cell ICP-MS to address the role of trace elements at a cellular level

The heterogeneity properties shown by cells or unicellular organisms have led to the development of analytical methods at the single-cell level. In this sense, considering the importance of trace elements in these biological systems, the inductively coupled plasma mass spectrometer (ICP-MS) configured for analyzing single cell has presented a high potential to assess the evaluation of elements in cells. Moreover, advances in instrumentation, such as coupling laser ablation to the tandem configuration (ICP-MS/MS), or alternative mass analyzers (ICP-SFMS and ICP-TOFMS), brought significant benefits, including sensitivity improvement, high-resolution imaging, and the cell fingerprint. From this perspective, the single-cell ICP-MS has been widely reported in studies involving many fields, from oncology to environmental research. Hence, it has contributed to finding important results, such as elucidating nanoparticle toxicity at the cellular level and vaccine development. Therefore, in this review, the theory of single-cell ICP-MS analysis is explored, and the applications in this field are pointed out. In addition, the instrumentation advances for single-cell ICP-MS are addressed.