DNA binding specificities of the long zinc-finger recombination protein PRDM9

Background

Meiotic recombination ensures proper segregation of homologous chromosomes and creates genetic variation. In many organisms, recombination occurs at limited sites, termed 'hotspots', whose positions in mammals are determined by PR domain member 9 (PRDM9), a long-array zinc-finger and chromatin-modifier protein. Determining the rules governing the DNA binding of PRDM9 is a major issue in understanding how it functions.

Results

Mouse PRDM9 protein variants bind to hotspot DNA sequences in a manner that is specific for both PRDM9 and DNA haplotypes, and that in vitro binding parallels its in vivo biological activity. Examining four hotspots, three activated by Prdm9^Cst and one activated by Prdm9^Dom2, we found that all binding sites required the full array of 11 or 12 contiguous fingers, depending on the allele, and that there was little sequence similarity between the binding sites of the three Prdm9^Cst activated hotspots. The binding specificity of each position in the Hlx1 binding site, activated by Prdm9^Cst, was tested by mutating each nucleotide to its three alternatives. The 31 positions along the binding site varied considerably in the ability of alternative bases to support binding, which also implicates a role for additional binding to the DNA phosphate backbone.

Conclusions

These results, which provide the first detailed mapping of PRDM9 binding to DNA and, to our knowledge, the most detailed analysis yet of DNA binding by a long zinc-finger array, make clear that the binding specificities of PRDM9, and possibly other long-array zinc-finger proteins, are unusually complex.

The circadian clock of Neurospora crassa

Circadian clocks organize our inner physiology with respect to the external world, providing life with the ability to anticipate and thereby better prepare for major fluctuations in its environment. Circadian systems are widely represented in nearly all major branches of life, except archaebacteria, and within the eukaryotes, the filamentous fungus Neurospora crassa has served for nearly half a century as a durable model organism for uncovering the basic circadian physiology and molecular biology. Studies using Neurospora have clarified our fundamental understanding of the clock as nested positive and negative feedback loops regulated through transcriptional and post-transcriptional processes. These feedback loops are centered on a limited number of proteins that form molecular complexes, and their regulation provides a physical explanation for nearly all clock properties. This review will introduce the basics of circadian rhythms, the model filamentous fungus N. crassa, and provide an overview of the molecular components and regulation of the circadian clock.

The glucagon-like peptide 1 receptor is essential for postprandial lipoprotein synthesis and secretion in hamsters and mice

AIMS/HYPOTHESIS

Glucagon-like peptide 1 (GLP-1) receptor (GLP-1R) agonists and dipeptidyl peptidase-4 (DPP-4) inhibitors attenuate postprandial lipaemia through mechanisms that remain unclear. As dyslipidaemia is a contributing risk factor for cardiovascular disease in type 2 diabetes, we examined the mechanisms linking pharmacological and physiological regulation of GLP-1 action to control of postprandial lipid metabolism.

METHODS

Postprandial lipid synthesis and secretion were assessed in normal and fructose-fed hamsters and in wild-type mice that were treated with or without sitagliptin. Apolipoprotein B-48 (ApoB-48) synthesis and secretion were also examined in primary enterocyte cultures. The importance of exogenous vs endogenous GLP-1R signalling for regulation of intestinal lipoprotein synthesis and secretion was assessed in mice and hamsters treated with the GLP-1R agonist exendin-4, the GLP-1R antagonist exendin(9-39) and in Glp1r (+/+) vs Glp1r (-/-) mice.

RESULTS

Sitagliptin decreased fasting plasma triacylglycerol, predominantly in the VLDL fraction, as well as postprandial triacylglycerol-rich lipoprotein (TRL)-triacylglycerol, TRL-cholesterol and TRL-ApoB-48 in hamsters and mice. GLP-1R activation with exendin-4 alone also decreased plasma and TRL-ApoB-48 in hamsters and mice, and reduced secretion of ApoB-48 in hamster enterocyte cultures. Conversely, blockade of endogenous GLP-1R signalling by the antagonist exendin(9-39) or genetic elimination of GLP-1R signalling in Glp1r (-/-) mice enhanced TRL-ApoB-48 secretion in vivo. Co-administration of exendin(9-39) also abolished the hypolipidaemic effect of sitagliptin.

CONCLUSIONS/INTERPRETATION

Potentiation of endogenous incretin action via DPP-4 inhibition or pharmacological augmentation of GLP-1R signalling reduces intestinal secretion of triacylglycerol, cholesterol and ApoB-48. Moreover, endogenous GLP-1R signalling is essential for the control of intestinal lipoprotein biosynthesis and secretion.

Post-translational modifications in circadian rhythms

The pace has quickened in circadian biology research. In particular, an abundance of results focused on post-translational modifications (PTMs) is sharpening our view of circadian molecular clockworks. PTMs affect nearly all aspects of clock biology; in some cases they are essential for clock function and in others, they provide layers of regulatory fine-tuning. Our goal is to review recent advances in clock PTMs, help make sense of emerging themes, and spotlight intriguing (and perhaps controversial) new findings. We focus on PTMs affecting the core functions of eukaryotic clocks, in particular the functionally related oscillators in Neurospora crassa, Drosophila melanogaster, and mammalian cells.

Glucagon-like peptide-2 increases intestinal lipid absorption and chylomicron production via CD36

BACKGROUND & AIMS

Excessive postprandial lipemia is a prevalent condition that results from intestinal oversecretion of apolipoprotein B48 (apoB48)-containing lipoproteins. Glucagon-like peptide-2 (GLP-2) is a gastrointestinal-derived intestinotropic hormone that links nutrient absorption to intestinal structure and function. We investigated the effects of GLP-2 on intestinal lipid absorption and lipoprotein production.

METHODS

Intestinal lipid absorption and chylomicron production were quantified in hamsters, wild-type mice, and Cd36(-/-) mice infused with exogenous GLP-2. Newly synthesized apoB48 was metabolically labelled in primary hamster jejunal fragments. Fatty acid absorption was measured, and putative fatty acid transporters were assessed by immunoblotting.

RESULTS

Human GLP-2 increased secretion of the triglyceride (TG)-rich lipoprotein (TRL)-apoB48 following oral administration of olive oil to hamsters; TRL and cholesterol mass each increased 3-fold. Fast protein liquid chromatography profiling indicated that GLP-2 stimulated secretion of chylomicron/very low-density lipoprotein-sized particles. Moreover, GLP-2 directly stimulated apoB48 secretion in jejunal fragments cultured ex vivo, increased expression of fully glycosylated cluster of differentiation 36/fatty acid translocase (CD36), and induced intestinal absorption of [(3)H]triolein. The ability of GLP-2 to increase intestinal lipoprotein production was lost in Cd36(-/-) mice.

CONCLUSIONS

GLP-2 stimulates intestinal apoB48-containing lipoprotein secretion, possibly through increased lipid uptake, via a pathway that requires CD36. These findings suggest that GLP-2 represents a nutrient-dependent signal that regulates intestinal lipid absorption and the assembly and secretion of TRLs from intestinal enterocytes.

Quantitative proteomics reveals a dynamic interactome and phase-specific phosphorylation in the Neurospora circadian clock

Circadian systems are comprised of multiple proteins functioning together to produce feedback loops driving robust, approximately 24 hr rhythms. In all circadian systems, proteins in these loops are regulated through myriad physically and temporally distinct posttranslational modifications (PTMs). To better understand how PTMs impact a circadian oscillator, we implemented a proteomics-based approach by combining purification of endogenous FREQUENCY (FRQ) and its interacting partners with quantitative mass spectrometry (MS). We identify and quantify time-of-day-specific protein-protein interactions in the clock and show how these provide a platform for temporal and physical separation between the dual roles of FRQ. Additionally, by unambiguously identifying over 75 phosphorylated residues, following their quantitative change over a circadian cycle, and examining the phenotypes of strains that have lost these sites, we demonstrate how spatially and temporally regulated phosphorylation has opposing effects directly on overt circadian rhythms and FRQ stability.

A role for casein kinase 2 in the mechanism underlying circadian temperature compensation

Temperature compensation of circadian clocks is an unsolved problem with relevance to the general phenomenon of biological compensation. We identify casein kinase 2 (CK2) as a key regulator of temperature compensation of the Neurospora clock by determining that two long-standing clock mutants, chrono and period-3, displaying distinctive alterations in compensation encode the beta1 and alpha subunits of CK2, respectively. Reducing the dose of these subunits, particularly beta1, significantly alters temperature compensation without altering the enzyme's Q(10). By contrast, other kinases and phosphatases implicated in clock function do not play appreciable roles in temperature compensation. CK2 exerts its effects on the clock by directly phosphorylating FREQUENCY (FRQ), and this phosphorylation is compromised in CK2 hypomorphs. Finally, mutation of certain putative CK2 phosphosites on FRQ, shown to be phosphorylated in vivo, predictably alters temperature compensation profiles effectively phenocopying CK2 mutants.

Circadian output, input, and intracellular oscillators: insights into the circadian systems of single cells

Circadian output comprises the business end of circadian systems in terms of adaptive significance. Work on Neurospora pioneered the molecular analysis of circadian output mechanisms, and insights from this model system continue to illuminate the pathways through which clocks control metabolism and overt rhythms. In Neurospora, virtually every strain examined in the context of rhythms bears the band allele that helps to clarify the overt rhythm in asexual development. Recent cloning of band showed it to be an allele of ras-1 and to affect a wide variety of signaling pathways yielding enhanced light responses and asexual development. These can be largely phenocopied by treatments that increase levels of intracellular reactive oxygen species. Although output is often unidirectional, analysis of the prd-4 gene provided an alternative paradigm in which output feeds back to affect input. prd-4 is an allele of checkpoint kinase-2 that bypasses the requirement for DNA damage to activate this kinase; FRQ is normally a substrate of activated Chk2, so in Chk2(PRD-4), FRQ is precociously phosphorylated and the clock cycles more quickly. Finally, recent adaptation of luciferase to fully function in Neurospora now allows the core FRQ/WCC feedback loop to be followed in real time under conditions where it no longer controls the overt rhythm in development. This ability can be used to describe the hierarchical relationships among FRQ-Less Oscillators (FLOs) and to see which are connected to the circadian system. The nitrate reductase oscillator appears to be connected, but the oscillator controlling the long-period rhythm elicited upon choline starvation appears completely disconnected from the circadian system; it can be seen to run with a very long noncompensated 60-120-hour period length under conditions where the circadian FRQ/WCC oscillator continues to cycle with a fully compensated circadian 22-hour period.

A circadian clock in Neurospora: how genes and proteins cooperate to produce a sustained, entrainable, and compensated biological oscillator with a period of about a day

Neurospora has proven to be a tractable model system for understanding the molecular bases of circadian rhythms in eukaryotes. At the core of the circadian oscillatory system is a negative feedback loop in which two transcription factors, WC-1 and WC-2, act together to drive expression of the frq gene. WC-2 enters the promoter region of frq coincident with increases in frq expression and then exits when the cycle of transcription is over, whereas WC-1 can always be found there. FRQ promotes the phosphorylation of the WCs, thereby decreasing their activity, and phosphorylation of FRQ then leads to its turnover, allowing the cycle to reinitiate. By understanding the action of light and temperature on frq and FRQ expression, the molecular basis of circadian entrainment to environmental light and temperature cues can be understood, and recently a specific role for casein kinase 2 has been found in the mechanism underlying circadian temperature-compensation. These data promise molecular explanations for all of the canonical circadian properties of this model system, providing biochemical answers and regulatory logic that may be extended to more complex eukaryotes including humans.

The Neurospora checkpoint kinase 2: a regulatory link between the circadian and cell cycles

The clock gene period-4 (prd-4) in Neurospora was identified by a single allele displaying shortened circadian period and altered temperature compensation. Positional cloning followed by functional tests show that PRD-4 is an ortholog of mammalian checkpoint kinase 2 (Chk2). Expression of prd-4 is regulated by the circadian clock and, reciprocally, PRD-4 physically interacts with the clock component FRQ, promoting its phosphorylation. DNA-damaging agents can reset the clock in a manner that depends on time of day, and this resetting is dependent on PRD-4. Thus, prd-4, the Neurospora Chk2, identifies a molecular link that feeds back conditionally from circadian output to input and the cell cycle.

Prevalence of negative-pressure pulmonary edema at an orthopaedic hospital

Negative-pressure pulmonary edema (NPPE) occurs when a large, negative intrathoracic pressure is generated against an obstructed upper airway, causing fluid to shift into the lung interstitium. Young, healthy, athletic male patients appear to be at increased risk for this disorder, but the prevalence in orthopaedic surgery patients has been unknown. We retrospectively reviewed the charts of 14 patients (11 male, 3 female) with NPPE at our institution over a 15-year period. The patients had 11 different surgical procedures; 16,653 similar procedures were done during this time. The overall prevalence of NPPE (< 0.1%) was not significantly different between male and female patients. Patients with NPPE were significantly younger than those without NPPE. If NPPE is recognized promptly and treated appropriately with intravenous diuretic and oxygen therapy, most patients respond well. Physicians should be vigilant to the potential for NPPE in young, otherwise healthy patients after general anesthesia.

Initial biomechanical properties of anterior cruciate ligament reconstruction autografts

To provide more information to consider when selecting a reconstruction technique, we did a side-by-side comparison of some of the initial biomechanical properties of currently accepted reconstruction methods. Our research hypotheses were that a quadrupled, woven semitendinosus and gracilis graft is as strong as any of the other commonly used graft materials and that quadrupling and weaving the hamstring graft may increase the stiffness of the overall construct Using lower extremity cadaveric specimens harvested from young donors, we fashioned seven each of seven types of graft: 9-mm, 10-mm, and 11-mm-wide patellar tendon graft (PTG); 10-mm-wide central quadriceps tendon graft; doubled semitendinosus graft; tripled semitendinosus graft; and quadrupled, woven semitendinosus and gracilis graft. Specimens were stripped of remaining soft tissue, and anterior cruciate ligament (ACL) constructs were created for biomechanical testing. The tibia was translated anteriorly on the femur, mimicking a pivot shift maneuver, andfailure strength, failure mechanism, and construct stiffness were recorded. No differences in mean strength were detected. The quadrupled, woven graft was significantly stiffer than the doubled semitendinosus graft and no less stiff than any of the PTG constructs. All grafts showed similar and adequate initial absolute strength to reconstruct the ACL. Quadrupling and weaving the semitendinosus and gracilis graft increases the stiffness of the reconstructed specimen to a level statistically similar to that of specimens reconstructed with a PTG.

Processing of second-order stimuli in the visual cortex

Naturally occurring visual stimuli are rich in examples of objects delineated from their backgrounds simply by differences in luminance, so-called first-order stimuli, as well as those defined by differences of contrast or texture, referred to as second-order stimuli. Here we provide a brief overview of visual cortical processing of second-order stimuli, as well as some comparative background on first-order processing, concentrating on single-unit neurophysiology, but also discussing relationships to human psychophysics and to neuroimaging. The selectivity of visual cortical neurons to orientation, spatial frequency, and direction of movement of first-order, luminance-defined stimuli is conventionally understood in terms of simple linear filter models, albeit with some minor nonlinearities such as thresholding and gain control. However, these kinds of models fail entirely to account for responses of neurons to second-order stimuli such as contrast envelopes, illusory contours, or texture borders. Second-order stimuli constructed from sinusoidal components have been used to analyze the neurophysiological mechanisms of such responses; these experiments demonstrate that the same neuron can exhibit three distinct kinds of tuning to spatial frequency, and also to orientation. These results can be understood in terms of a type of nonlinear 'filter-->rectify-->filter' model, which has been widely used in human psychophysics. Finally, several general issues will be discussed, including potential artifacts in experiments with second-order stimuli, and strategies for avoiding or controlling for them; caveats about definitions of first- vs. second-order mechanisms and stimuli; the concept of form-cue invariance; and the functional significance of second-order processing.

Centrifugal bias for second-order but not first-order motion

Limited-lifetime Gabor stimuli were used to assess both first- and second-order motion in peripheral vision. Both first- and second-order motion mechanisms were present at a 20-deg eccentricity. Second-order motion, unlike first-order, exhibits a bias for centrifugal motion, suggesting a role for the second-order mechanism in optic flow processing.

Lateral epicondylitis

Satisfactory treatment of lateral epicondylitis results from correct diagnosis followed by a well-controlled operative or nonoperative treatment program. Many options for nonoperative and operative treatment exist for lateral epicondylitis. More study is needed on outcomes of both nonoperative treatment and operative treatment so that each patient can attain maximal improvement. Balanced assessments of specific patient populations, along with definitions of the optimal treatment for each group, are required. This will allow physicians to integrate the available information and improve patient care.

Linear filtering and nonlinear interactions in direction-selective visual cortex neurons: a noise correlation analysis

Spatial and temporal properties related to direction selectivity of both simple and complex type visual cortex neurons were assessed by cross-correlation analysis of their responses to random ternary white noise. This stimulus consisted of multiple randomly placed bars, each colored white, black, or gray with equal probability, which were rerandomized every 5-10 ms. A first-order cross-correlation analysis of a neuron's spike train with the spatiotemporal history of the stimulus provided an estimate of the neuron's linear spatiotemporal filtering properties. A nonlinear correlation analysis measured the amount of interaction for pair-wise combinations of bars as a function of their relative spatial and temporal separations. The spatiotemporal orientation of each of these functions was quantified using a "motion energy index" (MEI), which was compared to the neurons' direction selectivity measured with drifting sinewave gratings. Both first-order and nonlinear correlation plots usually showed s-t orientation whose sign was consistent with the neuron's direction preference; however, in many cases the MEI for first-order analysis was weak compared to that seen in the nonlinear interactions. The structures of the nonlinear interaction functions were also compared with predictions from a conventional model of direction selectivity based on a simple spatiotemporally oriented linear filter, followed by an intensive nonlinearity ("LN model"). These comparisons showed that some neurons' data agreed reasonably well with such a model, while others agreed poorly or not at all. Simulations of an alternative model which combines signals from idealized lagged and nonlagged front-end linear filters produce noise correlation results more like those seen in the neurophysiological data.

Arthroscopic classification and treatment of lateral epicondylitis: two-year clinical results

We assessed the clinical utility of 42 arthroscopic releases for lateral epicondylitis in 40 patients (average age, 43 years) with an average of 14 months of symptomatic history before surgery. At arthroscopy, we found 15 type I lesions (intact capsule), 15 type II lesions (linear capsular tear), and 12 type III lesions (complete capsular tear), and associated disorders were found in 69% of the patients. At an average follow-up of 2.8 years, patients were asked to report on elbow pain and function. Subjectively, the patients rated their pain at rest as an average of 0.9 (0 = no pain; 10 = severe pain). They rated their pain with activities of daily living as 1.4 and their pain with sports and work as 1.9. Functionally, they averaged 11.1 of 12 possible points. Of the 39 elbows in the 37 patients who were available for follow-up, 37 were rated "better" or "much better." Patients returned to work in an average of 2.2 weeks. Grip strength averaged 96% of the strength of the unaffected limb. Arthroscopic tennis elbow release is a reliable treatment that allows patients an expedited return to work and may result in greater postsurgical grip strength.

Absence of a chromatic linear motion mechanism in human vision

We have investigated motion mechanisms in central and perifoveal vision using two-frame random Gabor kinematograms with isoluminant red-green or luminance stimuli. In keeping with previous results, we find that performance dominated by a linear motion mechanism is obtained using high densities of micropatterns and small temporal intervals between frames, while nonlinear performance is found with low densities and longer temporal intervals [Boulton, J. C., & Baker, C. L. (1994) Proceedings of SPIE, computational vision based on neurobiology, 2054, 124-133]. We compare direction discrimination and detection thresholds in the presence of variable luminance and chromatic noise. Our results show that the linear motion response obtained from chromatic stimuli is selectively masked by luminance noise; the effect is selective for motion since luminance noise masks direction discrimination thresholds but not stimulus detection. Furthermore, we find that chromatic noise has the reverse effect to luminance noise: detection thresholds for the linear chromatic stimulus are masked by chromatic noise but direction discrimination is relatively unaffected. We thus reveal a linear 'chromatic' mechanism that is susceptible to luminance noise but relatively unaffected by color noise. The nonlinear chromatic mechanism behaves differently since both detection and direction discrimination are unaffected by luminance noise but masked by chromatic noise. The double dissociation between the effects of chromatic and luminance noise on linear and nonlinear motion mechanisms is not based on stimulus speed or differences in the temporal presentations of the stimuli. We conclude that: (1) 'chromatic' linear motion is solely based on a luminance signal, probably arising from cone-based temporal phase shifts; (2) the nonlinear chromatic motion mechanism is purely chromatic; and (3) we find the same results for both perifoveal and foveal presentations.

Clinical Evaluation of the Athlete's Shoulder

OBJECTIVE

To describe the history and physical examination of the athlete's shoulder.

BACKGROUND

The complex, highly mobile shoulder joint is very susceptible to athletic injury. A comprehensive history and physical examination lay the groundwork for accurate decision making about the nature of the injury and the appropriate treatment plan.

DESCRIPTION

In taking the history,inquire about the patient's lifestyle (dominant hand, occupation, sports, activity level) and then focus on the specific complaint. Ask about the location, quality, and nature of the pain and activities that provoke the pain. If stiffness is a factor, a review of systems and the patient's past medical history are important. Discuss any previously undertaken interventions and their effects. The physical examination consists of inspection, range of motion, palpation, manual muscle testing, and provocative tests.

CLINICAL ADVANTAGES

Once the clinical evaluation has been completed, the nature of the injury will, in most cases, be apparent. If necessary, appropriate diagnostic tests are ordered, and then a treatment plan tailored to the athlete and the injury is instituted.

Anterior cruciate ligament reconstruction: socioeconomic issues and cost effectiveness

Anterior cruciate ligament ruptures continue to occur in increasing numbers. These injuries and their treatment create significant social and economic problems for patients, their physicians, and for society. By critically evaluating the trade-off between the costs and benefits of various treatment options, one can define a cost-effective approach to the management of this problem. Limited available data suggest that anterior cruciate ligament reconstruction is a highly cost-effective method of treatment for active young adults. The cost per additional quality-adjusted life year provided by surgery compares favorably with figures associated with other highly utilized health care interventions. Such data may prove invaluable within the context of health care reform.

A new anatomical landmark for reliable identification of human area V5/MT: a quantitative analysis of sulcal patterning

The location of human area V5 (or MT) has been correlated with the intersection of the ascending limb of the inferior temporal sulcus (ALITS) and the lateral occipital sulcus (LO). This study was undertaken to attempt a replication and quantification of these observations using functional magnetic resonance imaging. V5 was significantly activated in 19 hemispheres with alternating, low contrast, random checkerboard patterns. We confirmed the stereotaxic location of V5 and were able to describe a fairly consistent sulcal pattern in the parieto-temporo-occipital cortex. V5 was usually (95%) buried within a sulcus, most commonly within the inferior temporal sulcus (ITS) (11%), the ascending limb of the ITS (ALITS) (53%) and the posterior continuation of the ITS (26%). The average distance from V5 of two identified anatomical landmarks of V5, the junctions of the LO and the ALITS, and the ITS and ALITS, were both 1 cm. However, the LO-ALITS junction often had to be determined by interpolation (47%), and was not always present even with interpolation (21%). In contrast, the ITS-ALITS junction was always present and V5 was usually (90%) located in a sulcus intersecting with this junction, making it a more reliable landmark for localizing V5 with respect to gross morphological features on individual cortical surfaces.

Cost effectiveness of anterior cruciate ligament reconstruction in young adults

The cost effectiveness of ligament reconstruction for acute anterior cruciate ligament tears in young adults was compared with the cost effectiveness of nonoperative management. A decision tree was constructed to predict the expected functional outcomes for operative and nonoperative treatment. Outcome probabilities were derived from the surgical and natural history literature. Cost data were based on averaged figures from the senior author's institution. Utility values were determined from a questionnaire administered to 285 local university students. Cost effectiveness was calculated in terms of dollars spent per additional quality adjusted life year provided by the surgical reconstruction for the initial 7 years after an injury. The operative strategy provided 5.10 quality adjusted life years versus 3.49 years for nonoperative treatment, yielding a marginal effectiveness of 1.61 quality adjusted life years. The estimated total costs of the operative and nonoperative strategies were $11,768 and $2333, respectively, for a marginal cost of $9435. The resulting marginal cost effectiveness ratio was $5857 per quality adjusted life year. These data suggest that, when based on functional outcomes, anterior cruciate ligament reconstruction is a cost effective method of treatment for acute tears in young adults. The cost effectiveness ratio predicted compares favorably with those of other health care interventions that aim to improve quality of life.