Site-specific 2D IR spectroscopy: a general approach for the characterization of protein dynamics with high spatial and temporal resolution

The conformational heterogeneity and dynamics of protein side chains contribute to function, but investigating exactly how is hindered by experimental challenges arising from the fast timescales involved and the spatial heterogeneity of protein structures. The potential of two-dimensional infrared (2D IR) spectroscopy for measuring conformational heterogeneity and dynamics with unprecedented spatial and temporal resolution has motivated extensive effort to develop amino acids with functional groups that have frequency-resolved absorptions to serve as probes of their protein microenvironments. We demonstrate the full advantage of the approach by selective incorporation of the probe p-cyanophenylalanine at six distinct sites in a Src homology 3 domain and the application of 2D IR spectroscopy to site-specifically characterize heterogeneity and dynamics and their contribution to cognate ligand binding. The approach revealed a wide range of microenvironments and distinct responses to ligand binding, including at the three adjacent, conserved aromatic residues that form the recognition surface of the protein. Molecular dynamics simulations performed for all the labeled proteins provide insight into the underlying heterogeneity and dynamics. Similar application of 2D IR spectroscopy and site-selective probe incorporation will allow for the characterization of heterogeneity and dynamics of other proteins, how heterogeneity and dynamics are affected by solvation and local structure, and how they might contribute to biological function.

Functional connectivity in category-selective brain networks after encoding predicts subsequent memory

Activity in category selective regions of the temporal and parietal lobes during encoding has been associated with subsequent memory for face and scene stimuli. Reactivation theories of memory consolidation predict that after encoding connectivity between these category-selective regions and the hippocampus should be modulated and predict recognition memory. However, support for this proposal has been limited in humans. Here, participants completed a resting-state functional MRI (fMRI) scan, followed by face- and place-encoding tasks, followed by another resting-state fMRI scan during which they were asked to think about the stimuli they had previously encountered. Individual differences in face recognition memory were predicted by the degree to which connectivity between face-responsive regions of the fusiform gyrus and perirhinal cortex increased following the face-encoding task. In contrast, individual differences in scene recognition were predicted by connectivity between the hippocampus and a scene-selective region of the retrosplenial cortex before and after the place-encoding task. Our results provide novel evidence for category specificity in the neural mechanisms supporting memory consolidation.

The neural representation of social status in the extended face-processing network

Social status is a salient cue that shapes our perceptions of other people and ultimately guides our social interactions. Despite the pervasive influence of status on social behavior, how information about the status of others is represented in the brain remains unclear. Here, we tested the hypothesis that social status information is embedded in our neural representations of other individuals. Participants learned to associate faces with names, job titles that varied in associated status, and explicit markers of reputational status (star ratings). Trained stimuli were presented in an functional magnetic resonance imaging experiment where participants performed a target detection task orthogonal to the variable of interest. A network of face-selective brain regions extending from the occipital lobe to the orbitofrontal cortex was localized and served as regions of interest. Using multivoxel pattern analysis, we found that face-selective voxels in the lateral orbitofrontal cortex - a region involved in social and nonsocial valuation, could decode faces based on their status. Similar effects were observed with two different status manipulations - one based on stored semantic knowledge (e.g., different careers) and one based on learned reputation (e.g., star ranking). These data suggest that a face-selective region of the lateral orbitofrontal cortex may contribute to the perception of social status, potentially underlying the preferential attention and favorable biases humans display toward high-status individuals.

Geschwind Syndrome in frontotemporal lobar degeneration: Neuroanatomical and neuropsychological features over 9 years

Geschwind Syndrome, a characteristic behavioral syndrome frequently described in patients affected by temporal lobe epilepsy (TLE), consists of the following features: hyper-religiosity, hypergraphia, hyposexuality, and irritability. Here we report the 9-year-clinical course of a case of Geschwind Syndrome that developed as a first and salient clinical expression of right temporal lobe variant of frontotemporal lobar degeneration (FTLD). Only one patient affected by frontotemporal dementia has previously been shown to present with Geschwind Syndrome. MS presented at age 73 with 3 years of personality and behavioral symptoms. Her early symptoms primarily included hyper-religiosity, hypergraphia, and poor emotional regulation (irritability, impulsivity, disinhibition, egocentric behavior). Over nine years, other cognitive functions (word retrieval, memory coding and recall, set-shifting, famous face and building recognition) became affected; however, hyper-religiosity, hypergraphia, and scarce emotional control remained her most prominent deficits. Longitudinal cortical thickness and volumetric analyses revealed early atrophy in the right temporal pole, right amygdala, and right hippocampus, which progressively affected homologous regions in the left hemisphere. The present case describes an unusual clinical picture associated with frontotemporal dementia (FTD), in which the most salient symptoms originated and remained consistent with Geschwind Syndrome.

Focal temporal pole atrophy and network degeneration in semantic variant primary progressive aphasia

A wealth of neuroimaging research has associated semantic variant primary progressive aphasia with distributed cortical atrophy that is most prominent in the left anterior temporal cortex; however, there is little consensus regarding which region within the anterior temporal cortex is most prominently damaged, which may indicate the putative origin of neurodegeneration. In this study, we localized the most prominent and consistent region of atrophy in semantic variant primary progressive aphasia using cortical thickness analysis in two independent patient samples (n = 16 and 28, respectively) relative to age-matched controls (n = 30). Across both samples the point of maximal atrophy was located in the same region of the left temporal pole. This same region was the point of maximal atrophy in 100% of individual patients in both semantic variant primary progressive aphasia samples. Using resting state functional connectivity in healthy young adults (n = 89), we showed that the seed region derived from the semantic variant primary progressive aphasia analysis was strongly connected with a large-scale network that closely resembled the distributed atrophy pattern in semantic variant primary progressive aphasia. In both patient samples, the magnitude of atrophy within a brain region was predicted by that region's strength of functional connectivity to the temporopolar seed region in healthy adults. These findings suggest that cortical atrophy in semantic variant primary progressive aphasia may follow connectional pathways within a large-scale network that converges on the temporal pole.

More Than Meets the Eye: The Merging of Perceptual and Conceptual Knowledge in the Anterior Temporal Face Area

An emerging body of research has supported the existence of a small face sensitive region in the ventral anterior temporal lobe (ATL), referred to here as the "anterior temporal face area". The contribution of this region in the greater face-processing network remains poorly understood. The goal of the present study was to test the relative sensitivity of this region to perceptual as well as conceptual information about people and objects. We contrasted the sensitivity of this region to that of two highly-studied face-sensitive regions, the fusiform face area (FFA) and the occipital face area (OFA), as well as a control region in early visual cortex (EVC). Our findings revealed that multivoxel activity patterns in the anterior temporal face area contain information about facial identity, as well as conceptual attributes such as one's occupation. The sensitivity of this region to the conceptual attributes of people was greater than that of posterior face processing regions. In addition, the anterior temporal face area overlaps with voxels that contain information about the conceptual attributes of concrete objects, supporting a generalized role of the ventral ATLs in the identification and conceptual processing of multiple stimulus classes.

Knowledge is power: how conceptual knowledge transforms visual cognition

In this review, we synthesize the existing literature demonstrating the dynamic interplay between conceptual knowledge and visual perceptual processing. We consider two theoretical frameworks that demonstrate interactions between processes and brain areas traditionally considered perceptual or conceptual. Specifically, we discuss categorical perception, in which visual objects are represented according to category membership, and highlight studies showing that category knowledge can penetrate early stages of visual analysis. We next discuss the embodied account of conceptual knowledge, which holds that concepts are instantiated in the same neural regions required for specific types of perception and action, and discuss the limitations of this framework. We additionally consider studies showing that gaining abstract semantic knowledge about objects and faces leads to behavioral and electrophysiological changes that are indicative of more efficient stimulus processing. Finally, we consider the role that perceiver goals and motivation may play in shaping the interaction between conceptual and perceptual processing. We hope to demonstrate how pervasive such interactions between motivation, conceptual knowledge, and perceptual processing are in our understanding of the visual environment, and to demonstrate the need for future research aimed at understanding how such interactions arise in the brain.

Beyond the FFA: The role of the ventral anterior temporal lobes in face processing

Extensive research has supported the existence of a specialized face-processing network that is distinct from the visual processing areas used for general object recognition. The majority of this work has been aimed at characterizing the response properties of the fusiform face area (FFA) and the occipital face area (OFA), which together are thought to constitute the core network of brain areas responsible for facial identification. Although accruing evidence has shown that face-selective patches in the ventral anterior temporal lobes (vATLs) are interconnected with the FFA and OFA, and that they play a role in facial identification, the relative contribution of these brain areas to the core face-processing network has remained unarticulated. Here we review recent research critically implicating the vATLs in face perception and memory. We propose that current models of face processing should be revised such that the ventral anterior temporal lobes serve a centralized role in the visual face-processing network. We speculate that a hierarchically organized system of face processing areas extends bilaterally from the inferior occipital gyri to the vATLs, with facial representations becoming increasingly complex and abstracted from low-level perceptual features as they move forward along this network. The anterior temporal face areas may serve as the apex of this hierarchy, instantiating the final stages of face recognition. We further argue that the anterior temporal face areas are ideally suited to serve as an interface between face perception and face memory, linking perceptual representations of individual identity with person-specific semantic knowledge.

U. S. consumer perceptions of U. S. and Canadian beef quality grades

A U.S. consumer (n = 642) study (Baltimore, MD; Phoenix, AZ; and Lubbock, TX) was conducted to compare consumer sensory scores of U.S. beef (83 USDA Choice [Choice] and 96 USDA Select [Select]) and Canadian beef (77 AAA and 82 AA) strip loins. Strip loins (n = 338) were obtained from beef processors in Canada and the United States and were wet aged until 21 d postmortem at 2°C. Marbling scores were assigned at 21 d and loins were paired according to quality grades and marbling score. Strip loins were fabricated into 2.54-cm thick steaks; steaks were vacuum packaged and frozen until further evaluations. Proximate analysis was performed to compare fat, moisture, and protein. Choice and Canadian AAA had similar marbling scores and intramuscular fat. Both Choice and Canadian AAA had greater (P < 0.05) marbling scores and intramuscular fat than Canadian AA, but Select strip loins had intermediate values that were not different from any of the other grades (P > 0.05). Consumers' opinions did not differ when comparing equivalent grades (Choice with Canadian AAA and Select with Canadian AA), but they rated Choice and Canadian AAA more palatable than Select and Canadian AA for all sensory attributes (P < 0.05). Regarding percentage of acceptability and likelihood to buy score, consumers indicated a preference and greater probability to buy (P = 0.001 and P = 0.004, respectively) strip loin steaks from higher quality grade carcasses (Choice and Canadian AAA) than lower quality grade carcasses (Select and Canada AA). Additionally, consumers gave their opinion of Canadian beef, where its quality and safety were rated as "good" to "excellent" for both attributes (76.72% and 88.36%, respectively; P < 0.05), feeling confident in beef that is imported from Canada. In the same way, consumers indicated that country-of-origin labeling was a minimal factor influencing their beef steak purchasing decisions. Results from this consumer study indicated U.S. consumers could not differentiate between U.S. and Canadian beef within comparable quality grades; however, strip loin steaks from higher quality grades were more palatable than lower quality grades according to consumer scores for eating quality traits.

Use of qualitative methods to identify solutions to selected equine welfare problems in Ireland

This paper explores the views of those in the Irish equine industry, organisations and government regarding necessary improvements to equine welfare in Ireland at unregulated gatherings and during the disposal process. Three qualitative research methods were employed, namely semistructured interviews, focus groups and a structured, facilitated workshop. Representatives from industry, welfare societies, socially disadvantaged groupings and government engaged with this process and shared their views regarding horse welfare and implementable solutions with merit to address welfare problems. A consensus was achieved that equine welfare in Ireland could be improved by the development of a comprehensive identification system, a Code of Practice for horse gatherings, a horse licensing scheme, ring-fenced funding to promote responsible, humane horse disposal and better means of raising awareness of the value of safeguarding horse welfare for the benefit of all parties.

Are patient characteristics associated with the accuracy of hysterosalpingography in diagnosing tubal pathology? An individual patient data meta-analysis

BACKGROUND

Conventional meta-analysis has estimated the sensitivity and specificity of hysterosalpingography (HSG) to be 65% and 83%. The impact of patient characteristics on the accuracy of HSG is unknown. The aim of this study was to assess by individual patient data meta-analysis whether the accuracy of HSG is associated with different patient characteristics.

METHODS

We approached authors of primary studies reporting on the accuracy of HSG using findings at laparoscopy as the reference. We assessed whether patient characteristics such as female age, duration of subfertility and a clinical history without risk factors for tubal pathology were associated with the accuracy of HSG, using a random intercept logistic regression model.

RESULTS

We acquired data of seven primary studies containing data of 4521 women. Pooled sensitivity and specificity of HSG were 53% and 87% for any tubal pathology and 46% and 95% for bilateral tubal pathology. In women without risk factors, the sensitivity of HSG was 38% for any tubal pathology, compared with 61% in women with risk factors (P = 0.005). For bilateral tubal pathology, these rates were 13% versus 47% (P = 0.01). For bilateral tubal pathology, the sensitivity of HSG decreased with age [factor 0.93 per year (P = 0.05)]. The specificity of HSG was very stable across all subgroups.

CONCLUSIONS

The accuracy of HSG in detecting tubal pathology was similar in all subgroups, except for women without risk factors in whom sensitivity was lower, possibly due to false-positive results at laparoscopy. HSG is a useful tubal patency screening test for all infertile couples.

Harvestman (Opiliones) fauna associated with Maine lowbush blueberry fields in the major production areas of Washington and Hancock counties

Over a period of 19 yr, the harvestman (Opiliones) community associated with the lowbush blueberry agro-ecosystem in Maine was studied. Eight species representing five genera, four subfamilies, and two families of harvestmen belonging to the suborder Eupnoi were collected. The harvestman community was dominated by two introduced, synanthropic species: Phalangium opilio in all but 1 yr (that year dominated by Rilaena triangularis). Rilaena was recorded for the first time from eastern North America. Relative abundance of harvestman adults increases throughout the season and the temporal pattern of trap capture does not refute speculated life cycles of the harvestmen being univoltine with overwintering eggs. Some blueberry management practices were found to affect trap capture. We did find that on average (with opposite results 1 yr) trap captures are greater in pruned fields than in fruit-bearing fields. Organic fields were found to have higher relative abundance of harvestmen than conventionally managed fields. Conventionally managed fields with reduced-risk insecticides showed no difference in harvestmen relative abundance compared with those conventionally managed fields using the older more persistent organophosphate insecticides. Insecticide trials with common insecticides used in blueberry insect pest management showed that the organophosphate insecticide, phosmet, and the pyrethroid insecticide, esfenvalerate, were detrimental to P. opilio adults when exposed to leaf residues, whereas the reduced-risk insecticide, spinosad, showed no negative effects compared with nonsprayed foliage.

Unstable familial transmissions of Huntington disease alleles with 27-35 CAG repeats (intermediate alleles)

There are inconsistent reports regarding the likelihood of repeat instability for alleles with 27-35 CAG repeats in the Huntington disease (HD) gene. We have examined the intergenerational stability of such intermediate alleles in 51 families from the University of British Columbia's DNA and Tissue Bank for Huntington Disease Research (UBC-HD Databank). A total of 181 transmissions were identified, with 30% (n = 54/181) of the alleles being unstable upon transmission. The unstable transmissions included both expansions (n = 37) and contractions (n = 17) of CAG size. Of the expanded alleles, 68% (n = 25/37) expanded into the HD range (>36 CAG). Therefore, 14% (n = 25/181) of the 27-35 CAG allele transmissions examined expanded into the disease-associated range resulting in a new mutation for HD. Significantly, of these new mutations, 40% (n = 10/25) originated from an allele with 35 CAG repeats with CAG repeat expansions ranging from +1 CAG to +23 CAG. The proportion of new mutations in the UBC-HD Databank is consistent with the most recent new mutation rate for HD, estimated to be at least 10%. The observed difference in the stability of HD intermediate allele transmissions in this data set and in other studies may be a reflection of a small sample size. Alternately, these inconsistencies may indicate an underlying difference in genetic factors which influence repeat instability between the different populations examined. Additional studies determining the frequency and magnitude of repeat instability in this CAG repeat range and factors that influence instability are urgently needed. Until we understand the clinical implications of HD alleles with 27-35 CAG repeats and establish reliable risks of instability, we should exercise caution when translating these results to the clinic.

What is the most valid comparison treatment in trials of intrauterine insemination, timed or uninfluenced intercourse? A systematic review and meta-analysis of indirect evidence

BACKGROUND

Timed intercourse (TI), which is the usual control treatment in trials of intrauterine insemination (IUI), is not a typical coital activity and could impair fertility. This review summarizes the trials of IUI of male partner's prepared semen among subfertile couples according to whether the control group had TI or expectant management.

METHODS

A search of relevant databases and bibliographies until February 2008 yielded 150 citations of which 31 were potentially relevant and 11 met all criteria. The total estimates of the differences in pregnancy rates per couple were calculated with weights equal to the inverse variance. The primary analysis was a categorical meta-analysis by the type of control treatment (TI or expectant management).

RESULTS

In 11 trials with 13 comparisons of IUI and intercourse among 1329 couples with subfertility, the average difference in pregnancy rate between IUI and controls was 6.1% in trials with TI and 3.9% in trials with expectant management, as the control. The adjusted indirect estimate of the difference between the types of control groups was 2.8% (95% CI -6.3, 10.7). The difference by type of control treatment was not significant, neither in the 11 most relevant trials (P = 0.82), nor in a broader group of 19 trials and 2512 patients (P = 0.20).

CONCLUSIONS

The additional benefit accruing to IUI, where TI is the control, is not significant, but it is consistent with the possibility that pregnancy may be less likely in TI controls than in expectant management controls.

Karyotypic analysis of adult pluripotent stem cells

Three categories of precursor cells have been identified in postnatal mammals: tissue-committed progenitor cells, germ layer lineage-committed stem cells and lineage-uncommitted pluripotent stem cells. Progenitor cells are the immediate precursors of differentiated tissues. Germ layer lineage stem cells can be induced to form multiple cell types belonging to their respective ectodermal, mesodermal, and endodermal embryological lineages. Pluripotent stem cells will form somatic cell types from all three primary germ layer lineages. Progenitor cells demonstrate a finite life span before replicative senescence and cell death occur. Both germ layer lineage stem cells and pluripotent stem cells are telomerase positive and display extensive capabilities for self-renewal. Stem cells which undergo such extensive replication have the potential for undergoing mutations that may subsequently alter cellular functions. Gross mutations in the genome may be visualized as chromosomal aneuploidy and/or chromosomes that appear aberrant. This study was designed to determine whether any gross genomic mutations occurred within the adult pluripotent stem cells. Karyotypic analysis was performed using pluripotent stem cells purified from adult male rats using established procedures. Giemsa Banding was used in conjunction with light microscopy to visualize metaphase chromosome spreads. To date over 800 metaphase spreads have been analyzed. We found that the metaphase spreads averaged 42 chromosomes and concluded that these pluripotent stem cells isolated from adult rats have a normal karyotype.

Two new prediction rules for spontaneous pregnancy leading to live birth among subfertile couples, based on the synthesis of three previous models

BACKGROUND

Several models have been published for the prediction of spontaneous pregnancy among subfertile patients. The aim of this study was to broaden the empirical basis for these predictions by making a synthesis of three previously published models.

METHODS

We used the original data from the studies of Eimers et al. (1994), Collins et al. (1995) and Snick et al. (1997) on couples consulting for various forms of subfertility. We developed a so-called three-sample synthesis model for predicting spontaneous conception leading to live birth within 1 year after intake based on the three data sets. The predictors used are duration of subfertility, women's age, primary or secondary infertility, percentage of motile sperm, and whether the couple was referred by a general practitioner or by a gynaecologist (referral status). The performance of this model was assessed according to a 'jack-knife' analysis. Because the post-coital test (PCT) was not assessed in one of the samples, a synthesis model including the PCT was based on two samples only.

RESULTS

The ability of the synthesis models to distinguish between women who became pregnant and those who did not was comparable to the ability of the one-sample models when applied in the other samples. The reliability of the predictions by the three-sample synthesis model was somewhat better. Predictions improved considerably by including the PCT.

CONCLUSIONS

The synthesis models performed better and had a broader empirical basis than the original models. They are therefore better suitable for application in other centres.