Functional analysis of BLAP75, a BLM-associated protein

Bloom syndrome (BS) is an autosomal recessive disorder characterized by dwarfism, immunodeficiency, impaired fertility, and most importantly, early development of a broad range of cancers. The hallmark of BS cells is hyper-recombination, characterized by a drastically elevated frequency of sister chromatid exchange (SCE). BLM, the gene mutated in BS, encodes a DNA helicase of the RecQ protein family. BLM is thought to participate in several DNA transactions and to interact with many proteins involved in DNA replication, recombination, and repair. However, the precise function of BLM and the BLM-dependent anti-tumor mechanism remain obscure. ^ A novel protein, BLAP75 (BLM-associated polypeptide, 75KD), was identified to form an evolutionarily conserved complex with BLM and DNA topoisomerase IIIα (Topo IIIα). Our work demonstrates that loss of BLAP75 destabilized BLM and Topo IIIα proteins. BLAP75 colocalized with BLM in subnuclear foci in response to DNA damage and the recruitment of BLM to these foci was BLAP75-dependent. Moreover, depletion of BLAP75 by siRNA resulted in an elevated SCE rate similar to cells depleted of BLM by siRNA. In addition, RNAi-mediated silencing of BLAP75 greatly diminished cell viability. This cellular deficiency was rescued by expression of wild type BLAP75 but not BLAP75 with mutated conserved domain III, which abrogated the interaction between BLAP75, BLM and Topo IIIα, suggesting that the integrity of BLM-Topo IIIα-BLAP75 complex might be critical for cell survival. Finally, I found that BLAP75 was phosphorylated during mitosis and upon various DNA-damaging agents, implying that BLAP75 might also function in mitosis and DNA damage response. ^ Taken together, this study has defined BLAP75 as an integral component of the BLM complex to maintain genome stability. Our findings provide insights into the molecular mechanisms of the BLM helicase pathway and tumorigenesis process associated with these mechanisms. ^

Long-term gastrointestinal complications of Clostridium difficile associated diarrhea (CDAD)

Background. The incidence of Clostridium difficile -associated diarrhea (CDAD) is increasing worldwide likely because of increased use of broad spectrum antibiotics and the introduction of a clonal hyper-virulent strain called the BI strain. Short-term complications of CDAD include recurrent disease, requirement for colectomy, and persistent disease. However, data on the long-term consequences of CDAD are scarce. Among other infectious diseases (Shigella, Salmonella, and Campylobacter), long-term consequences such as irritable bowel syndrome (IBS), chronic dyspepsia/diarrhea, and other GI effects have been noted. Since the mechanism of action of these agents is similar to C.difficile, we hypothesized that patients with CDAD have greater likelihood of developing IBS and other functional gastrointestinal disorders (FGIDs) in the long-term as compared to a general sample of recently hospitalized patients. ^ Objective. To evaluate the long-term gastrointestinal complications of CDAD, (IBS, functional diarrhea, functional abdominal bloating, functional constipation and functional abdominal pain syndrome). ^ Methods. The current study was a secondary analysis of a previously completed observational case-control outcome study. Adult CDAD patients at St. Luke's Episcopal Hospital, Houston (SLEH) were followed up and interviewed by telephone six months after the initial diagnosis thereafter evaluated for the development of IBS and other FGIDs. A total of 46 patients with CDAD infection were recruited at SLEH between May-November 2007. The comparators were patients hospitalized in SLEH within one month before or after the admission of the reference case, hospital length of stay within one week longer or shorter than reference case, and age within 10 years more or less than the reference case. Cases and comparators were compared using Fisher's exact test. A p<0.05 was considered significant. ^ Results. Thirty CDAD patients responded to the questionnaires and were compared to 40 comparators. No comparator developed a FGID, while 3 (10%) CDAD patients developed new onset IBS (p=0.07), 4 (13.3%) developed new onset Functional Diarrhea (p=0.03), and 3 (10%) developed new onset Functional Constipation (p=0.07). No patient developed Functional Abdominal Bloating and Functional Abdominal Pain Syndrome. ^ Conclusion. In this study, new onset functional diarrhea was significantly more common in patients CDAD within six months after initial infection compared to matched controls.^

Caspase 8: Mediating the effects of a novel proteasome inhibitor, NPI-0052

Targeting the proteasome with the sole FDA approved proteasome inhibitor (PI), bortezomib, has been fruitful in specific cancers. Its success has generated an interest in next-generation PIs that might have a therapeutic advantage in cancers, such as leukemia, where bortezomib monotherapy was less effective. This study focuses on a novel, clinically relevant PI, NPI-0052. Experiments show that NPI-0052 targets chymotrypsin- and caspase-like activities more potently than the trypsin-like activity in leukemia cells. NPI-0052 induced apoptosis, as determined by caspase-3 activation and DNA fragmentation. Using caspase inhibitors and caspase-8 (I9.2) or FADD (I2.1) deficient cells revealed that caspase-8 was essential for NPI-0052-induced apoptosis. NPI-0052 killed cells via a caspase-8-tBid-mitochondrial pathway, relying on caspase-8, whereas bortezomib relies on several caspases. NPI-0052 increased reactive oxygen species (ROS) levels, which contributed towards cytotoxicity since an antioxidant conferred protection. To improve the clinical efficacy of PIs, NPI-0052 was combined with epigenetic anti-cancer agents, histone deacetylase inhibitors (HDACi). NPI-0052 with MS-275 or vorinostat (FDA approved HDACi), synergistically induced apoptosis more effectively than an HDACi/bortezomib regimen in Jurkat cells. Caspase-8 and ROS contributed towards NPI-0052/HDACi cytotoxicity and caspase-8 mediated superoxide production by NPI-0052 or NPI-0052/HDACi. The proximal targets of these agents: proteasome activity and histone acetylation were examined to determine if they contributed towards synergistic effects. HDACi targeted proteasomal β subunits and corresponding catalytic activities responsible for degrading proteins. Immunoblotting showed increases in histone-H3 expression and its acetylation with NPI-0052 or NPI-0052/HDACi in Jurkat and primary cells. Importantly, the hyper-acetylation by NPI-0052 was not detected with bortezomib, suggesting that this effect may be unique to NPI-0052. An antioxidant attenuated histone-H3 expression and acetylation induced by NPI-0052 alone or with HDACi. Furthermore, the hyper-acetylation by NPI-0052 relied on caspase-8. These novel results show that a PI is eliciting classical epigenetic alterations, demonstrated by hyper-acetylation of histone-H3. This alteration was oxidant and caspase-8 dependent. Overall, results reveal that caspase-8 mediates many effects induced by NPI-0052. Data show overlapping activities by NPI-0052 and HDACi which are contributing, along with caspase-8 activation and oxidative stress, to cytotoxic interactions in leukemia cells, reinforcing the potential clinical utility of combining these two compounds. ^

BIOMEDICAL LANGUAGE UNDERSTANDING AND EXTRACTION (BLUE-TEXT): A MINIMAL SYNTACTIC, SEMANTIC METHOD

Clinical text understanding (CTU) is of interest to health informatics because critical clinical information frequently represented as unconstrained text in electronic health records are extensively used by human experts to guide clinical practice, decision making, and to document delivery of care, but are largely unusable by information systems for queries and computations. Recent initiatives advocating for translational research call for generation of technologies that can integrate structured clinical data with unstructured data, provide a unified interface to all data, and contextualize clinical information for reuse in multidisciplinary and collaborative environment envisioned by CTSA program. This implies that technologies for the processing and interpretation of clinical text should be evaluated not only in terms of their validity and reliability in their intended environment, but also in light of their interoperability, and ability to support information integration and contextualization in a distributed and dynamic environment. This vision adds a new layer of information representation requirements that needs to be accounted for when conceptualizing implementation or acquisition of clinical text processing tools and technologies for multidisciplinary research. On the other hand, electronic health records frequently contain unconstrained clinical text with high variability in use of terms and documentation practices, and without commitmentto grammatical or syntactic structure of the language (e.g. Triage notes, physician and nurse notes, chief complaints, etc). This hinders performance of natural language processing technologies which typically rely heavily on the syntax of language and grammatical structure of the text. This document introduces our method to transform unconstrained clinical text found in electronic health information systems to a formal (computationally understandable) representation that is suitable for querying, integration, contextualization and reuse, and is resilient to the grammatical and syntactic irregularities of the clinical text. We present our design rationale, method, and results of evaluation in processing chief complaints and triage notes from 8 different emergency departments in Houston Texas. At the end, we will discuss significance of our contribution in enabling use of clinical text in a practical bio-surveillance setting.

CONFORMATIONAL DYNAMICS OF K-RAS AND H-RAS PROTEINS: IS THERE FUNCTIONAL SPECIFICITY AT THE CATALYTIC DOMAIN?

Ras proteins serve as crucial signaling modulators in cell proliferation through their ability to hydrolyze GTP and exist in a GTP “on” state and GTP “off” state. There are three different human Ras isoforms: H-ras, N-ras and K-ras (4A and 4B). Although their sequence identity is very high at the catalytic domain, these isoforms differ in their ability to activate different effectors and hence different signaling pathways. Much of the previous work on this topic has attributed this difference to the hyper variable region of Ras proteins, which contains most of the sequence variance among the isoforms and encodes specificity for differential distribution in the membrane. However, we hypothesize that sequence variation on lobe II of Ras catalytic domain alters dynamics and leads to differential preference for different effectors or modulators. In this work, we used all atom molecular dynamics to analyze the dynamics in the catalytic domain of H-ras and K-ras. We have also analyzed the dynamics of a transforming mutant of H-ras and K-ras and further studied the dynamics of an effectorselective mutant of H-ras. Collectively we have determined that wild type K-ras is more dynamic than H-ras and that the structure of the effector binding loop more closely resembles that of the T35S Raf-selective mutant, possibly giving us a new view and insight into the v mode of effector specificity. Furthermore we have determined that specific mutations at the same location perturb the conformational equilibrium differently in H-ras and K-ras and that an enhanced oncogenic potential may arise from different structural perturbations for each point mutation of a specific isoform.

Escape performance of temperate king scallop, Pecten maximus under ocean warming and acidification

Among bivalves, scallops are exceptional due to their capacity to escape from predators by swimming which is provided by rapid and strong claps that are produced by the phasic muscle interspersed with tonic muscle contractions. Based on the concept of oxygen and capacity-limited thermal tolerance, the following hypothesis was tested: ocean warming and acidification (OWA) would induce disturbances in aerobic metabolic scope and extracellular acid-case status and impair swimming performance in temperate scallops. Following long-term incubation under near-future OWA scenarios [20 vs. 10 °C (control) and 0.112 kPa CO2 (hypercapnia) vs. 0.040 kPa CO2 (normocapnic control)], the clapping performance and metabolic rates (MR) were measured in resting (RMR) and fatigued (maximum MR) king scallops, Pecten maximus, from Roscoff, France. Exposure to OA, either alone or combined with warming, left MR and swimming parameters such as the total number of claps and clapping forces virtually unchanged. Only the duration of the escape response was affected by OA which caused earlier exhaustion in hyper- than in normocapnic scallops at 10 °C. While maximum MR was unaffected, warm exposure increased RMR in both normocapnic and hypercapnic P. maximus resulting in similar Q 10 values of ~2.2. The increased costs of maintenance and the observation of strongly reduced haemolymph PO2 levels indicate that at 20 °C scallops have reached the upper thermal pejus range with unbalanced capacities for aerobic energy metabolism. As a consequence, warming to 20 °C decreased mean phasic force during escape performance until fatigue. The observed prolonged recovery time in warm incubated scallops might be a consequence of elevated metabolic costs at reduced oxygen availability in the warmth.

De la identidad a las intersubjetividades en la comunicación mundo : Elementos para el debate

El documento tiene como pretensión, en un primer momento, establecer líneas de diferenciación entre la ciencia clásica y la ciencia contemporánea, develando las lógicas convencionales de la razón positiva y sus dinámicas instrumentales, que no favorecen los espacios para la comprensión ni el reconocimiento de la misma comprensión (preocupada, ciertamente, por la hiperespecialización y la binarización de la cotidianidad).

Prisiones textuales. Artificio y violencia enla poesía española del barroco

En busca de una nueva lengua artificial, Góngora trata de restituir con medios poéticos una similitud entre palabras y cosas. Así, en el soneto «Prisión del nácar era articulado¼ (1620), en el que artificio y violencia están correlacionados, la artificialidad de la misma descripción corresponde a lo artificial de la belleza descrita. Las técnicas gongorinas desempeñan aquí una función mimológica, por la cual el texto parece hacer visible y audible una violencia que desde siempre subyace en el elogio lírico de la dama. Su imagen «hiperpreciosa¼ debe su belleza sobresaliente a una constricción masculina. Este rasgo es reelaborado por otros poetas barrocos como Quevedo.

Frank Willaert, Herman Braet, Thom Mertens y Theo Venckeleer, eds., Medieval Memory. Image and Text , Turnhout: Brepols, Fédération Internationale des Instituts d'Études Médiévales, Textes et Études duMoyen Âge, 27, 2004

Fil: Disalvo, Santiago Aníbal. Universidad Nacional de La Plata. Facultad de Humanidades y Ciencias de la Educación; Argentina.

Text Comprehension And roduction in University Students: Text Reformulation

This paper sets out to report on findings about features of task-specific reformulation observed in university students in the middle stretch of the Psychology degree course (N=58) and in a reference group of students from the degree courses in Modern Languages, Spanish and Library Studies (N=33) from the National University of La Plata (Argentina). Three types of reformulation were modeled: summary reformulation, comprehensive and productive reformulation.The study was based on a corpus of 621 reformulations rendered from different kinds of text. The versions obtained were categorised according to the following criteria: presence or absence of normative, morphosyntactic and semantic difficulties. Findings show that problems arise particularly with paraphrase and summary writing. Observation showed difficulties concerning punctuation, text cohesion and coherence , and semantic distortion or omission as regards extracting and/or substituting gist, with limited lexical resources and confusion as to suitability of style/register in writing. The findings in this study match those of earlier, more comprehensive research on the issue and report on problems experienced by a significant number of university students when interacting with both academic texts and others of a general nature. Moreover, they led to questions, on the one hand, as to the nature of such difficulties, which appear to be production-related problems and indirectly account for inadequate text comprehension, and on the other hand, as to the features of university tuition when it comes to text handling.

High-resolution ice thickness and bed topography of a land-terminating section of the Greenland Ice Sheet, with links to GeoTIFFs and text files

We present ice thickness and bed topography maps with a high spatial resolution (250-500 m) of a land-terminating section of the Greenland Ice Sheet derived from ground-based and airborne radar surveys. The data have a total area of ~12 000 km^2 and cover the whole ablation area of the outlet glaciers of Isunnguata Sermia, Russell, Leverett, Ørkendalen and Isorlersuup up to the long-term mass balance equilibrium line altitude at ~1600 m above sea level. The bed topography shows highly variable subglacial trough systems, and the trough of Isunnguata Sermia Glacier is overdeepened and reaches an elevation of ~500 m below sea level. The ice surface is smooth and only reflects the bedrock topography in a subtle way, resulting in a highly variable ice thickness. The southern part of our study area consists of higher bed elevations compared to the northern part. The compiled data sets of ground-based and airborne radar surveys cover one of the most studied regions of the Greenland Ice Sheet and can be valuable for detailed studies of ice sheet dynamics and hydrology.

De la identidad a las intersubjetividades en la comunicación mundo : Elementos para el debate

El documento tiene como pretensión, en un primer momento, establecer líneas de diferenciación entre la ciencia clásica y la ciencia contemporánea, develando las lógicas convencionales de la razón positiva y sus dinámicas instrumentales, que no favorecen los espacios para la comprensión ni el reconocimiento de la misma comprensión (preocupada, ciertamente, por la hiperespecialización y la binarización de la cotidianidad).

Prisiones textuales. Artificio y violencia enla poesía española del barroco

En busca de una nueva lengua artificial, Góngora trata de restituir con medios poéticos una similitud entre palabras y cosas. Así, en el soneto «Prisión del nácar era articulado¼ (1620), en el que artificio y violencia están correlacionados, la artificialidad de la misma descripción corresponde a lo artificial de la belleza descrita. Las técnicas gongorinas desempeñan aquí una función mimológica, por la cual el texto parece hacer visible y audible una violencia que desde siempre subyace en el elogio lírico de la dama. Su imagen «hiperpreciosa¼ debe su belleza sobresaliente a una constricción masculina. Este rasgo es reelaborado por otros poetas barrocos como Quevedo.

Frank Willaert, Herman Braet, Thom Mertens y Theo Venckeleer, eds., Medieval Memory. Image and Text , Turnhout: Brepols, Fédération Internationale des Instituts d'Études Médiévales, Textes et Études duMoyen Âge, 27, 2004

Fil: Disalvo, Santiago Aníbal. Universidad Nacional de La Plata. Facultad de Humanidades y Ciencias de la Educación; Argentina.

Text Comprehension And roduction in University Students: Text Reformulation

This paper sets out to report on findings about features of task-specific reformulation observed in university students in the middle stretch of the Psychology degree course (N=58) and in a reference group of students from the degree courses in Modern Languages, Spanish and Library Studies (N=33) from the National University of La Plata (Argentina). Three types of reformulation were modeled: summary reformulation, comprehensive and productive reformulation.The study was based on a corpus of 621 reformulations rendered from different kinds of text. The versions obtained were categorised according to the following criteria: presence or absence of normative, morphosyntactic and semantic difficulties. Findings show that problems arise particularly with paraphrase and summary writing. Observation showed difficulties concerning punctuation, text cohesion and coherence , and semantic distortion or omission as regards extracting and/or substituting gist, with limited lexical resources and confusion as to suitability of style/register in writing. The findings in this study match those of earlier, more comprehensive research on the issue and report on problems experienced by a significant number of university students when interacting with both academic texts and others of a general nature. Moreover, they led to questions, on the one hand, as to the nature of such difficulties, which appear to be production-related problems and indirectly account for inadequate text comprehension, and on the other hand, as to the features of university tuition when it comes to text handling.