Dinucleotides as simple models of the base stacking-unstacking component of DNA 'breathing' mechanisms.

Regulatory protein access to the DNA duplex 'interior' depends on local DNA 'breathing' fluctuations, and the most fundamental of these are thermally-driven base stacking-unstacking interactions. The smallest DNA unit that can undergo such transitions is the dinucleotide, whose structural and dynamic properties are dominated by stacking, while the ion condensation, cooperative stacking and inter-base hydrogen-bonding present in duplex DNA are not involved. We use dApdA to study stacking-unstacking at the dinucleotide level because the fluctuations observed are likely to resemble those of larger DNA molecules, but in the absence of constraints introduced by cooperativity are likely to be more pronounced, and thus more accessible to measurement. We study these fluctuations with a combination of Molecular Dynamics simulations on the microsecond timescale and Markov State Model analyses, and validate our results by calculations of circular dichroism (CD) spectra, with results that agree well with the experimental spectra. Our analyses show that the CD spectrum of dApdA is defined by two distinct chiral conformations that correspond, respectively, to a Watson-Crick form and a hybrid form with one base in a Hoogsteen configuration. We find also that ionic structure and water orientation around dApdA play important roles in controlling its breathing fluctuations.

Critical review of brain AVM surgery, surgical results and natural history in 2017.

BACKGROUND: An understanding of the present standing of surgery, surgical results and the role in altering the future morbidity and mortality of untreated brain arteriovenous malformations (bAVMs) is appropriate considering the myriad alternative management pathways (including radiosurgery, embolization or some combination of treatments), varying risks and selection biases that have contributed to confusion regarding management. The purpose of this review is to clarify the link between the incidence of adverse outcomes that are reported from a management pathway of either surgery or no intervention with the projected risks of surgery or no intervention. METHODS: A critical review of the literature was performed on the outcomes of surgery and non-intervention for bAVM. An analysis of the biases and how these may have influenced the outcomes was included to attempt to identify reasonable estimates of risks. RESULTS: In the absence of treatment, the cumulative risk of future hemorrhage is approximately 16% and 29% at 10 and 20 years after diagnosis of bAVM without hemorrhage and 35% and 45% at 10 and 20 years when presenting with hemorrhage (annualized, this risk would be approximately 1.8% for unruptured bAVMs and 4.7% for 8 years for bAVMs presenting with hemorrhage followed by the unruptured bAVM rate). The cumulative outcome of these hemorrhages depends upon whether the patient remains untreated and is allowed to have a further hemorrhage or is treated at this time. Overall, approximately 42% will develop a new permanent neurological deficit or death from a hemorrhagic event. The presence of an associated proximal intracranial aneurysm (APIA) and restriction of venous outflow may increase the risk for subsequent hemorrhage. Other risks for increased risk of hemorrhage (age, pregnancy, female) were examined, and their purported association with hemorrhage is difficult to support. Both the Spetzler-Martin grading system (and its compaction into the Spetzler-Ponce tiers) and Lawton-Young supplementary grading system are excellent in predicting the risk of surgery. The 8-year risk of unfavorable outcome from surgery (complication leading to a permanent new neurological deficit with a modified Rankin Scale score of greater than one, residual bAVM or recurrence) is dependent on bAVM size, the presence of deep venous drainage (DVD) and location in critical brain (eloquent location). For patients with bAVMs who have neither a DVD nor eloquent location, the 8-year risk for an unfavorable outcome increases with size (increasing from 1 cm to 6 cm) from 1% to 9%. For patients with bAVM who have either a DVD or eloquent location (but not both), the 8-year risk for an unfavorable outcome increases with the size (increasing from 1 cm to 6 cm) from 4% to 35%. For patients with bAVM who have both a DVD and eloquent location, the 8-year risk for unfavorable outcome increases with size (increasing from 1 cm to 3 cm) from 12% to 38%. CONCLUSION: Patients with a Spetzler-Ponce A bAVM expecting a good quality of life for the next 8 years are likely to do better with surgery in expert centers than remaining untreated. Ongoing research is urgently required on the outcome of management pathways for bAVM.

Distinctive microbiomes and metabolites linked with weight loss after gastric bypass, but not gastric banding.

Roux-en-Y gastric bypass (RYGB) and laparoscopic adjustable gastric banding (LAGB) are anatomically different bariatric operations. RYGB achieves greater weight loss compared with LAGB. Changes in the gut microbiome have been documented after RYGB, but not LAGB, and the microbial contribution to sustainable surgical weight loss warrants further evaluation. We hypothesized that RYGB imposes greater changes on the microbiota and its metabolism than LAGB, and that the altered microbiota may contribute to greater weight loss. Using multi-omic approaches, we analyzed fecal microbial community structure and metabolites of pre-bariatric surgery morbidly obese (PreB-Ob), normal weight (NW), post-RYGB, and post-LAGB participants. RYGB microbiomes were significantly different from those from NW, LAGB and PreB-Ob. Microbiome differences between RYGB and PreB-Ob populations were mirrored in their metabolomes. Diversity was higher in RYGB compared with LAGB, possibly because of an increase in the abundance of facultative anaerobic, bile-tolerant and acid-sensible microorganisms in the former. Possibly because of lower gastric acid exposure, phylotypes from the oral cavity, such as Escherichia, Veillonella and Streptococcus, were in greater abundance in the RYGB group, and their abundances positively correlated with percent excess weight loss. Many of these post-RYGB microorganisms are capable of amino-acid fermentation. Amino-acid and carbohydrate fermentation products-isovalerate, isobutyrate, butyrate and propionate-were prevalent in RYGB participants, but not in LAGB participants. RYGB resulted in greater alteration of the gut microbiome and metabolome than LAGB, and RYGB group exhibited unique microbiome composed of many amino-acid fermenters, compared with nonsurgical controls.

Transdural arterial recruitment to brain arteriovenous malformation: clinical and management implications in a prospective cohort series.

OBJECTIVE The occurrence of transdural arterial recruitment (TDAR) in association with brain arteriovenous malformation (bAVM) is uncommon, and the reason for TDAR is not understood. The aim of this cohort study was to examine patient and bAVM characteristics associated with TDAR and the implications of TDAR on management. METHODS A prospective surgical database of bAVMs was examined. Cases previously treated elsewhere or incompletely examined by digital subtraction angiography (DSA) assessment were excluded. Three studies of this cohort were performed, as follows: characteristics associated with TDAR, the relationship between TDAR and neurological deficits unassociated with hemorrhage (NDUH), and the impact of TDAR on outcome from surgery. Regression models were performed. RESULTS Of 769 patients with complete DSA who had no previous treatment, 51 (6.6%) were found to have TDAR. The presence of TDAR was associated with increasing age (p < 0.01; OR 1.05; 95% CI 1.02-1.07); presentation with NDUH (p < 0.01; OR 2.71; 95% CI 1.29-5.71); increasing size of the bAVM (p < 0.01; OR 1.57; 95% CI 1.29-1.91); and combined supply from both anterior and posterior circulations (p = 0.02; OR 2.37; 95% CI 1.17-4.78). Further analysis of TDAR cases comparing those with and without NDUH found an association of larger size (6.6 cm [2.9 SD] compared with 4.7 cm [1.8 SD]; p < 0.01) and combined supply from both anterior and posterior circulations (relative risk 2.5; 95% CI 1.0-6.2; p = 0.04) to be associated with an NDUH presentation. For the 632 patients undergoing surgery there was an increased risk of complications (where this produced a new permanent neurological deficit at 12 months represented by a modified Rankin Scale score of > 1) with the following variables: size; location in eloquent brain; deep venous drainage; increasing age; and no presentation with hemorrhage. The presence of TDAR was not associated with an increased risk of complications from surgery. CONCLUSIONS The authors found that TDAR occurs in older patients with larger bAVMs, and that TDAR is also more likely to be associated with bAVMs presenting with NDUH. The likely explanation for the presence of TDAR is a secondary recruitment arising as a consequence of shear stress, rather than a primary vascular supply present from the earliest development of the bAVM.

A single-molecule view of the assembly pathway, subunit stoichiometry, and unwinding activity of the bacteriophage T4 primosome (helicase-primase) complex.

Single-molecule fluorescence resonance energy transfer (smFRET) methods were used to study the assembly pathway and DNA unwinding activity of the bacteriophage T4 helicase-primase (primosome) complex. The helicase substrates used were surface-immobilized model DNA replication forks "internally" labeled in the duplex region with opposed donor/acceptor (iCy3/iCy5) chromophore pairs in the lagging and leading strands. The time dependence of the smFRET signals was monitored during the unwinding process, and helicase rates and processivities were measured as a function of GTP concentration. This smFRET approach was also used to investigate the subunit stoichiometry of the primosome and the assembly pathway required to form functional and fully active primosome-DNA complexes. We confirmed that gp41 helicase monomer subunits form stable hexameric helicases in the presence of GTP and that the resulting (gp41)(6) complexes bind only weakly at DNA fork junctions. The addition of a single subunit of gp61 primase stabilized the resulting primosome complex at the fork and resulted in fully active and processive primosome helicases with gp41:gp61 subunit ratios of 6:1, while higher and lower subunit ratios substantially reduced the primosome unwinding activity. The use of alternative assembly pathways resulted in a loss of helicase activity and the formation of metastable DNA-protein aggregates, which were easily detected in our smFRET experiments as intense light-scattering foci. These single-molecule experiments provide a detailed real-time visualization of the assembly pathway and duplex DNA unwinding activity of the T4 primosome and are consistent with more indirect equilibrium and steady state results obtained in bulk solution studies.

Cytoskeletal-assisted dynamics of the mitochondrial reticulum in living cells.

Subcellular organelle dynamics are strongly influenced by interactions with cytoskeletal filaments and their associated motor proteins, and lead to complex multiexponential relaxations that occur over a wide range of spatial and temporal scales. Here we report spatio-temporal measurements of the fluctuations of the mitochondrial reticulum in osteosarcoma cells by using Fourier imaging correlation spectroscopy, over time and distance scales of 10(-2) to 10(3) s and 0.5-2.5 microm. We show that the method allows a more complete description of mitochondrial dynamics, through the time- and length-scale-dependent collective diffusion coefficient D(k,tau), than available by other means. Addition of either nocodazole to disrupt microtubules or cytochalasin D to disassemble microfilaments simplifies the intermediate scattering function. When both drugs are used, the reticulum morphology of mitochondria is retained even though the cytoskeletal elements have been de-polymerized. The dynamics of the organelle are then primarily diffusive and can be modeled as a collection of friction points interconnected by elastic springs. This study quantitatively characterizes organelle dynamics in terms of collective cytoskeletal interactions in living cells.

A replicating module as the unit of mitochondrial structure and functioning.

The mitochondrion within human cells in tissue culture is pleomorphic and highly dynamic. The organelle mass can exist as thousands of small ovoids or as one continuous reticulum. In either state, the mitochondrial mass is in constant thermal motion, as well as moving in approximately 0.8-microm jumps that are determined by, and related to, attachments with cytoskeletal elements. Many protein complexes, such as the pyruvate dehydrogenase (PDH) complex and DNA containing nucleoids, are dispersed through the mass and as though fixed by attachments to membranes, such that they can become distributed to all of the individual small ovoid mitochondria when the reticulum becomes fragmented. This leads us to propose that a replicating module is the repeating unit of mitochondrial structure. Studies to examine heterogeneity of functioning within the organelle mass are briefly reviewed.