Identifying Potential Risks and Benefits of Using Cloud in Distributed Software Development.

Cloud-based infrastructure has been increasingly adopted by the industry in distributed software development (DSD) environments. Its proponents claim that its several benefits include reduced cost, increased speed and greater productivity in software development. Empirical evaluations, however, are in the nascent stage of examining both the benefits and the risks of cloud-based infrastructure. The objective of this paper is to identify potential benefits and risks of using cloud in a DSD project conducted by teams based in Helsinki and Madrid. A cross-case qualitative analysis is performed based on focus groups conducted at the Helsinki and Madrid sites. Participants observations are used to supplement the analysis. The results of the analysis indicated that the main benefits of using cloud are rapid development, continuous integration, cost savings, code sharing, and faster ramp-up. The key risks determined by the project are dependencies, unavailability of access to the cloud, code commitment and integration, technical debt, and additional support costs. The results revealed that if such environments are not planned and set up carefully, the benefits of using cloud in DSD projects might be overshadowed by the risks associated with it.

Business, development and inclusive supply chains. Exploring pathways for the sustainable incorporation of the poor as suppliers in agrifood supply chains

El panorama global está cambiando, y esto influye sobre la forma en la que entendemos y tratamos de alcanzar un desarrollo humano sostenible. El crecimiento de la población conlleva una mayor presión sobre los recursos, pero también supone una mayor cantidad de mano de obra y de talento; la concentración en áreas urbanas está cambiando las dinámicas sociales y desafiando los canales de comercialización tradicionales, pero también genera nuevos mercados y fomenta la innovación; los cambios en la economía global están reduciendo los tradicionales desequilibrios de poder entre los países occidentales y el resto del mundo; y las crecientes interconexiones crean nuevos riesgos pero también oportunidades para lanzar iniciativas de alcance global. Todas estas tendencias nos están obligando a repensar qué es el desarrollo humano y de qué manera deberíamos afrontar el reto de la pobreza. Es comúnmente aceptado que la globalización implica interdependencia y que, para conseguir un desarrollo humano sostenible, la colaboración entre actores de distintos ámbitos es necesaria. Se observa una creciente convergencia de temas, intereses y soluciones en torno al desarrollo sostenible, incluso en diferentes países y sectores, lo que está facilitando la colaboración estratégica entre empresas, gobiernos y sociedad civil. Existen pocas duda a día de hoy sobre el papel fundamental que las empresas deben desempeñar en la transición mundial hacia la sostenibilidad ambiental y la erradicación de la pobreza. Las empresas están evolucionando desde un enfoque tradicional centrado en la maximización de beneficios económicos hacia un enfoque holístico que integra la sostenibilidad y la responsabilidad social como parte del núcleo de negocio de las compañías. En el ámbito medioambiental, muchas empresas ya han comenzado a actuar y tratan de reducir sus emisiones, sus desechos y su consumo de energía. Sin embargo la contribución de las empresas a la reducción de la pobreza no está tan clara. Actualmente en torno a 1,2 miles de millones de personas viven en situación de extrema pobreza. La mayoría de estas personas aún vive en zonas rurales donde la mayor parte de la población activa trabaja en el sector agrícola. Por lo tanto, mejorar las oportunidades y reducir los riesgos de los productores más vulnerables en el sector de la agricultura puede ser un motor de desarrollo rural y reducción de la pobreza, especialmente en países de bajo nivel de desarrollo cuyas economías están fundamentalmente basadas en la agricultura. Algunas empresas comienzan a incluir a los pobres en sus operaciones como consumidores, proveedores y emprendedores. Esta tesis se centra en las potenciales oportunidades relacionadas con la incorporación sostenible de los pobres como proveedores de productos y/o de mano de obra. La colaboración entre empresas y productores vulnerables de países en desarrollo es un tema relativamente nuevo y todavía poco estudiado. La pregunta que guía esta tesis es: “¿Cómo pueden las empresas facilitar la inclusión sostenible en cadenas de suministro de productores vulnerables de los países menos desarrollados?”. Para responder a la pregunta anterior, la autora ha aplicado una metodología de casos de estudio. Esta metodología se considera apropiada porque la investigación sobre cadenas de suministro inclusivas es todavía escasa y porque es necesario entender en profundidad un fenómeno de la vida real, y para ello es fundamental conocer su contexto. En primer lugar, se realiza una revisión de literatura para identificar las proposiciones y los constructos teóricos que guiarán la posterior recogida de datos. La revisión de literatura se divide en dos partes: una más general que explora la dimensión social de la sostenibilidad en cadenas de suministro, y una más específica que se centra en la incorporación de los pobres como proveedores en cadenas de suministro. A lo largo de la última década, ha habido un crecimiento exponencial de los estudios académicos sobre la sostenibilidad de las cadenas de suministro, pero la mayoría de los esfuerzos se han dirigido hacia la dimensión medioambiental de la sostenibilidad. Por lo tanto la revisión de literatura, que se presenta en la Sección 3.1 (página 35) y que profundiza en la sostenibilidad social de las cadenas de suministro, puede considerarse una contribución en sí misma. Esta revisión de literatura revela que la investigación sobre aspectos sociales en cadenas de suministro está cobrando impulso en distintas áreas de conocimiento, principalmente en los ámbitos de investigación sobre “gestión de cadenas de suministro”, “responsabilidad social corporativa” y “estudios del desarrollo”. La investigación existente sobre sostenibilidad social de cadenas de suministro se centra en tres temas: aclarar la definición de sostenibilidad social; analizar la implementación de estrategias de sostenibilidad social en cadenas de suministro; y estudiar el apoyo de las em presas líderes a proveedores vulnerables para facilitar su transición hacia la sostenibilidad. Un marco conceptual que resume los principales hallazgos de esta primera parte de la revisión de literatura es planteado en la Figura 7 (página 48). No obstante, en el área de investigación que está emergiendo en torno a la sostenibilidad social de las cadenas de suministro, los estudios relacionados con la reducción de la pobreza son aún escasos. Además se aprecia una falta de contribuciones desde y sobre los países menos desarrollados, así como una clara tendencia a reflejar la visión de las empresas líderes de las cadenas de suministro, olvidando la perspectiva de los proveedores. La segunda parte de la revisión de literatura presentada en la Sección 3.2 (página 51) profundiza en tres líneas de investigación que exploran, desde distintas perspectivas, la inclusión de los pobres en cadenas de suministro. Estas líneas son “Global Value Chains” (GVC), “Base of the Pyramid” (BoP) y “Sustainable Supply Chain Management” (SSCM). La investigación en GVC analiza las cadenas de suministro desde la perspectiva de la globalización económica y el comercio internacional, poniendo especial énfasis en las implicaciones para los países en desarrollo y las comunidades vulnerables. GVC caracteriza las cadenas de suministro según la forma en la que son gobernadas, las oportunidades de mejora que existen para los productores que forman parte de la cadena y el grado de inclusión o exclusión de las comunidades más pobres y vulnerables. La investigación en BoP explora las relaciones comerciales entre empresas y comunidades pobres. La premisa fundamental del concepto BoP es la posibilidad de combinar la generación de beneficios con la reducción de la pobreza. La propuesta original es que mediante la venta de productos y servicios a las comunidades pobres de países en desarrollo, la pobreza puede ser reducida al tiempo que las empresas incrementan sus beneficios, especialmente las grandes empresas multinacionales. Esta idea ha ido evolucionando y, a día de hoy, los investigadores BoP consideran la incorporación de los pobres no sólo como consumidores sino también como empleados, proveedores y co-creadores. La investigación en SSCM ha estado fundamentalmente orientada al estudio de la dimensión medioambiental de la sostenibilidad de cadenas de suministro. Sin embargo, la creciente externalización de la producción a países en desarrollo y las demandas de los grupos de interés para que las empresas aborden todos los aspectos de la sostenibilidad han llevado a los académicos de SSCM a reconocer la importancia de integrar asuntos relacionados con la reducción de la pobreza en sus investigaciones. Algunos estudios comienzan a apuntar los principales retos a los que se enfrentan las empresas para colaborar con productores vulnerables en sus cadenas de suministro. Estos retos son: falta de comunicación, altos costes de transacción y el incremento de la complejidad de las operaciones. Las contribuciones de estas tres líneas de investigación son complementarias para el estudio de las cadenas de suministro inclusivas. Sin embargo, raramente han sido consideradas conjuntamente, ya que pertenecen a ámbitos de conocimiento distintos. Esta tesis integra las aportaciones de GVC, BoP y SSCM en un marco conceptual para la creación y gestión de cadenas de suministro inclusivas. Este marco conceptual para cadenas de suministro inclusivas queda representado en la Figura 9 (página 68). El marco conceptual refleja las motivaciones que llevan a las empresas a colaborar con productores vulnerables, los retos a los que se enfrentan al hacerlo, y los caminos o estrategias que están siguiendo para construir y operar cadenas de suministro inclusivas de manera que sean beneficiosas tanto para la empresa como para los productores vulnerables. A fin de validar y refinar el marco conceptual propuesto, tres casos de estudio se llevan a cabo. Las cadenas de suministro analizadas por los casos de estudio pertenecen al sector agrícola y sus principales proveedores se encuentran en países de África subsahariana. Múltiples métodos de recolección de datos y triangulación son utilizados para mejorar la fiabilidad de los datos. La autora desarrolló trabajos de campo en Senegal, Etiopía y Tanzania. Estos viajes permitieron enriquecer el proceso de recogida de información mediante entrevistas semiestructuradas y conversaciones informales con los principales actores de la cadena de suministro y mediante la observación directa de los procesos y las interacciones entre productores vulnerables y empresas. El Caso de estudio A (Sección 5.1 en página 96) es un caso de estudio único. Analiza la cadena de suministro local de verduras en Senegal. La organización focal es Manobi, una empresa senegalesa que provee servicios de bajo coste a emprendedores locales del sector agrícola. El Caso de estudio A proporciona un interesante análisis del funcionamiento de una cadena de suministro local en un país en desarrollo y muestra como la provisión de servicios profesionales puede mejorar el desempeño de productores vulnerables. El Caso de estudio B (Sección 5.2 en página 122) es un caso de estudio único. Analiza la cadena de suministro global de flor cortada con origen en Etiopía. La organización focal es EHPEA, la Asociación Etíope de Productores y Exportadores Hortícolas, cuya misión es promover y salvaguardar la posición competitiva del sector agrícola etíope en el mercado global. El Caso de estudio B ayuda a comprender mejor la perspectiva de los proveedores respecto a los requerimiento de sostenibilidad del mercado global. También muestra cómo la inclusión de los productores en el proceso de desarrollo de un estándar privado facilita su implementación posterior. El Caso de estudio C (Sección 5.3 en página 143) es un caso de estudio múltiple. Analiza la cadena de suministro global de café especial con origen en Tanzania. Las organizaciones focales son comerciantes que conectan de manera directa a pequeños agricultores de café en países en desarrollo con empresas tostadoras de café en países desarrollados. El Caso de estudio C muestra cómo un pequeño agricultor puede proveer un producto “premium” al mercado global, y participar en un segmento diferenciado del mercado a través de una cadena de suministro transparente y eficiente. Las aportaciones empíricas de los casos de estudio ayudan a validar y mejorar el marco conceptual sobre cadenas de suministro inclusivas (ver discusión en el Capítulo 6 en página 170). El resultado es la propuesta de una nueva versión del marco conceptual representado en la Figura 40 (página 195). Los casos de estudio también proporcionan interesantes aportaciones en relación a la gestión de cadenas de suministro inclusivas y muestran las perspectivas de distintos actores implicados. Esta tesis arroja luz sobre el papel de las empresas en la creación y la gestión de cadenas de suministro inclusivas llevando a cabo una revisión de literatura multidisciplinar y analizando tres casos de estudio en países africanos. Como resultado, esta tesis presenta una serie de contribuciones empíricas y teóricas al ámbito de investigación emergente en torno a las cadenas de suministro inclusivas (Capítulo 7). Esta tesis también pretende ser útil a profesionales que deseen facilitar la incorporación de los pobres como proveedores en condiciones justas y beneficiosas. ABSTRACT The global outlook is changing, and this is influencing the way we understand and try to achieve sustainable human development. Population growth entails increasing pressure over resources, but it also provides greater workforce and talent; concentration in urban areas is changing social dynamics and challenging traditional marketing channels, but also creating news markets and driving innovation; the global economy shift is rebalancing the traditional power imbalance between Western countries and the rest of the world, making new opportunities to arise; and interconnections and global interdependence create new risks but also opportunities for launching initiatives with a global reach. All these trends are impelling us to rethink what development is and in which way poverty alleviation should be approached. It is generally agreed that globalization implies interdependence and, in order to achieve sustainable human development, collaboration of all actors is needed. A convergence of issues, interests and solutions related to sustainable development is being observed across countries and sectors, encouraging strategic collaboration among companies, governments and civil society. There is little doubt nowadays about the crucial role of the private sector in the world’s path towards environmental sustainability and poverty alleviation. Businesses are evolving from a “business as usual” stance to a more sustainable and responsible approach. In the environmental arena, many companies have already “walk the talk”, implementing environmental management systems and trying to reduce emissions and energy consumption. However, regarding poverty alleviation, their contribution is less clear. There are around 1.2 billion people living in extreme poverty. Most of this people still live in rural areas where the agricultural sector employs a big part of the active population. Therefore, improving opportunities and reducing risks for vulnerable producers in the agri-food sector can be a primary engine of rural development and poverty alleviation, particularly in the poor, agriculture-based economies of least developed countries. Some companies are beginning to include the poor into their operations as consumers, suppliers and entrepreneurs. This thesis focuses specifically on the potential opportunities related to the sustainable incorporation of the poor as suppliers of products and/or labor. Business collaboration with vulnerable producers in developing countries is a relatively new trend and it is still understudied. The overall question guiding this thesis is: “How can businesses facilitate the sustainable inclusion of vulnerable producers from least developed countries into supply chains?”. In order to answer the research question, the author has applied a case study research strategy. This methodology is considered appropriate because research about inclusive supply chains is still at an early stage, and because there is a need to understand a real-life phenomenon in depth, but such understanding encompasses important contextual conditions. First, a literature review is conducted, in order to identify the research propositions and theoretical constructs that will guide the data collection. The literature review is divided in two parts: a more general one that explores the social dimension of sustainability of supply chains, and a more specific one that focuses on the incorporation of the poor as suppliers in supply chains. During the last decade, there has been an exponential growth of studies in the field of supply chain sustainability, but research efforts have traditionally been directed towards the analysis of the environmental dimension. Therefore, the literature review presented in Section 3.1 (page 35) that delves into social sustainability of supply chains can be considered a contribution in itself. This literature review reveals that the investigation of social issues in supply chains is gaining momentum and comes from different academic disciplines, namely Supply Chain Management, Corporate Social Responsibility and Development Studies. Existing research about social sustainability of supply chains focuses on three issues: clarify the definition of social sustainability; analyze the implementation of social sustainability strategies in supply chains; and study lead companies’ support to vulnerable suppliers in their transition towards sustainability. A conceptual framework that outlines the main findings that emerge from this first part of literature review is proposed in Figure 7 (page 48). Nevertheless, in this nascent field of social sustainability of supply chains, studies related to poverty alleviation are still scarce. Moreover, a lack of contributions from and about least developed countries has been observed, as well as a tendency to reflect on the lead firms’ standpoint, neglecting the suppliers’ perspective. The second part of the literature review (Section 3.2 in page 51) delves into three research streams that are exploring the inclusion of the poor into supply chains from different viewpoints. These research streams are Global Value Chains (GVC), Base of the Pyramid (BoP) and Sustainable Supply Chain Management (SSCM). GVC research discusses the dynamics of economic globalization and international trade, putting special emphasis in the implications for developing countries and vulnerable communities. GVC characterizes supply chains by the way they are governed, the upgrading opportunities that exist for producers in the chain and the degree of inclusion or exclusion of impoverished communities. BoP research explores trading relationships between businesses and impoverished communities. The core premise of the BoP concept is the possibility to combine profits with poverty alleviation. The original BoP proposition is that by marketing innovative products and services to poor communities in developing countries, poverty would be reduced and companies would increase their benefits, especially multinational companies. This idea has evolved to consider the incorporation of the poor to business activities not only as consumers, but also as employees, entrepreneurs and co-creators. The SSCM school of thought has mainly focused on studying the environmental dimension of supply chain sustainability, neglecting the consideration of the social perspective. However, in recent years, increasing outsourcing of production to developing countries and stakeholders’ demands for a more holistic approach to business sustainability have led SSCM scholars to acknowledge the importance of integrating poverty concerns in this field’s research agenda. Some SSCM studies identify the main operational challenges for companies which engage with vulnerable suppliers in their supply chains: missing communication, higher transactional and operational costs and increased complexity. Contributions from these three research streams are complementary for the study of inclusive supply chains. However, they have been rarely considered together, since they belong to different research areas. This thesis seeks to play a dovetailing role in this scenario by proposing a conceptual framework for creating and operating inclusive supply chains that builds on contributions from GVC, SSCM and BoP research. This framework for inclusive supply chains is depicted in Figure 9 (page 68), and explains the motivations that drive businesses to collaborate with vulnerable suppliers, the chal lenges they face in doing so, and the pathways they are following in order to build and operate inclusive supply chains profitably for both buying companies and vulnerable suppliers. In order to validate and refine the proposed framework, three case studies are carried out. The supply chains analyzed by the case studies belong to the agri-food sector and source from Sub-Saharan African countries. Multiple data collection methods and triangulation are used in order to improve reliability of findings. The author carried out field work in Senegal, Ethiopia and Tanzania. These travels enriched the data collection process, providing semi-structured interviews and informal conversations with the main actors in the supply chains, as well as direct observation of processes and interactions among companies and vulnerable suppliers. Case study A (Section 5.1 in page 96) is a single case study. It analyzes a local supply chain in Senegal providing vegetables to the local market. The focal organization is Manobi, a Senegalese inclusive business which provides affordable ICT services to local entrepreneurs in the agri-food sector. Case study A provides interesting insights into the dynamics of local supply chains and how professional services can help to improve their performance. Case study B (Section 5.2 in page 122) is a single case study. It analyzes a global supply chain with origin in Ethiopia providing cut flowers to the global commodity market. The focal organization is EHPEA, Ethiopian Horticulture Producers and Exporters Association, whose mission is to promote and safeguard the competitive position of the Ethiopian horticulture sector within the global market. Case study B helps to better understand the suppliers’ perspective regarding global market sustainability requirements and shows how the inclusion of suppliers in the process of development of a private standard has a positive impact in its implementation. Case study C (Section 5.3 in page 143) is a multiple case study. It analyzes a global supply chain with origin in Tanzania providing coffee to the global niche market of specialty coffee. The focal organizations are traders who are directly connecting smallholder coffee farmers in developing countries to coffee roasters in developed countries. Case study C shows how smallholder farmers can supply a premium product and be incorporated in a differentiated market segment through a transparent and efficient supply chain. The empirical findings from the case studies help to validate and refine the conceptual framework (see discussion in Chapter 6). The proposal of a new version of the conceptual framework is depicted in Figure 40 (page 195). The case studies also provide interesting insights related to the management of inclusive supply chains and show the perspectives of the different actors involved. This thesis sheds some light on the role of businesses in the creation and operation of inclusive supply chains by carrying out a cross-disciplinary literature review and analyzing three case studies in African countries. In doing so, this thesis presents a series of theoretical and empirical contributions to the emerging academic field of inclusive supply chains (Chapter 7). This thesis also intends to be useful to practitioners willing to improve the incorporation of the poor as suppliers in fair and profitable conditions.

Morphogenetic movements at gastrulation require the SH2 tyrosine phosphatase Shp2

The SH2 domain-containing tyrosine phosphatase Shp2 plays a pivotal role during the gastrulation of vertebrate embryos. However, because of the complex phenotype observed in mouse mutant embryos, the precise role of Shp2 during development is unclear. To define the specific functions of this phosphatase, Shp2 homozygous mutant embryonic stem cells bearing the Rosa-26 LacZ transgene were isolated and used to perform a chimeric analysis. Here, we show that Shp2 mutant cells amass in the tail bud of embryonic day 10.5 chimeric mouse embryos and that this accumulation begins at the onset of gastrulation. At this early stage, Shp2 mutant cells collect in the primitive streak of the epiblast and thus show deficiencies in their contribution to the mesoderm lineage. In high-contribution chimeras, we show that overaccumulation of Shp2 mutant cells at the posterior end of the embryo results in two abnormal phenotypes: spina bifida and secondary neural tubes. Consistent with a failure to undergo morphogenic movements at gastrulation, Shp2 is required for embryo fibroblast cells to mount a positive chemotactic response to acidic fibroblast growth factor in vitro. Our results demonstrate that Shp2 is required at the initial steps of gastrulation, as nascent mesodermal cells form and migrate away from the primitive streak. The aberrant behavior of Shp2 mutant cells at gastrulation may result from their inability to properly respond to signals initiated by fibroblast growth factors.

Control of pre-mRNA accumulation by the essential yeast protein Nrd1 requires high-affinity transcript binding and a domain implicated in RNA polymerase II association

Nrd1 is an essential yeast protein of unknown function that has an RNA recognition motif (RRM) in its carboxyl half and a putative RNA polymerase II-binding domain, the CTD-binding motif, at its amino terminus. Nrd1 mediates a severe reduction in pre-mRNA production from a reporter gene bearing an exogenous sequence element in its intron. The effect of the inserted element is highly sequence-specific and is accompanied by the appearance of 3′-truncated transcripts. We have proposed that Nrd1 binds to the exogenous sequence element in the nascent pre-mRNA during transcription, aided by the CTD-binding motif, and directs 3′-end formation a short distance downstream. Here we show that highly purified Nrd1 carboxyl half binds tightly to the RNA element in vitro with sequence specificity that correlates with the efficiency of cis-element-directed down-regulation in vivo. A large deletion in the CTD-binding motif blocks down-regulation but does not affect the essential function of Nrd1. Furthermore, a nonsense mutant allele that produces truncated Nrd1 protein lacking the RRM has a dominant-negative effect on down-regulation but not on cell growth. Viability of this and several other nonsense alleles of Nrd1 appears to require translational readthrough, which in one case is extremely efficient. Thus the CTD-binding motif of Nrd1 is important for pre-mRNA down-regulation but is not required for the essential function of Nrd1. In contrast, the RNA-binding activity of Nrd1 appears to be required both for down-regulation and for its essential function.

Mammalian capping enzyme binds RNA and uses protein tyrosine phosphatase mechanism

Mammalian capping enzymes are bifunctional proteins with both RNA 5′-triphosphatase and guanylyltransferase activities. The N-terminal 237-aa triphosphatase domain contains (I/V)HCXXGXXR(S/T)G, a sequence corresponding to the conserved active-site motif in protein tyrosine phosphatases (PTPs). Analysis of point mutants of mouse RNA 5′-triphosphatase identified the motif Cys and Arg residues and an upstream Asp as required for activity. Like PTPs, this enzyme was inhibited by iodoacetate and VO43− and independent of Mg2+, providing additional evidence for phosphate removal from RNA 5′ ends by a PTP-like mechanism. The full-length, 597-aa mouse capping enzyme and the C-terminal guanylyltransferase fragment (residues 211–597), unlike the triphosphatase domain, bound poly (U) and were nuclear in transfected cells. RNA binding was increased by GTP, and a guanylylation-defective, active-site mutant was not affected. Ala substitution at positions required for the formation of the enzyme-GMP capping intermediate (R315, R530, K533, or N537) also eliminated poly (U) binding, while proteins with conservative substitutions at these sites retained binding but not guanylyltransferase activity. These results demonstrate that the guanylyltransferase domain of mammalian capping enzyme specifies nuclear localization and RNA binding. Association of capping enzyme with nascent transcripts may act in synergy with RNA polymerase II binding to ensure 5′ cap formation.

A Z-DNA binding domain present in the human editing enzyme, double-stranded RNA adenosine deaminase

Editing of RNA changes the read-out of information from DNA by altering the nucleotide sequence of a transcript. One type of RNA editing found in all metazoans uses double-stranded RNA (dsRNA) as a substrate and results in the deamination of adenosine to give inosine, which is translated as guanosine. Editing thus allows variant proteins to be produced from a single pre-mRNA. A mechanism by which dsRNA substrates form is through pairing of intronic and exonic sequences before the removal of noncoding sequences by splicing. Here we report that the RNA editing enzyme, human dsRNA adenosine deaminase (DRADA1, or ADAR1) contains a domain (Zα) that binds specifically to the left-handed Z-DNA conformation with high affinity (KD = 4 nM). As formation of Z-DNA in vivo occurs 5′ to, or behind, a moving RNA polymerase during transcription, recognition of Z-DNA by DRADA1 provides a plausible mechanism by which DRADA1 can be targeted to a nascent RNA so that editing occurs before splicing. Analysis of sequences related to Zα has allowed identification of motifs common to this class of nucleic acid binding domain.

Preferential interaction of the his pause RNA hairpin with RNA polymerase β subunit residues 904–950 correlates with strong transcriptional pausing

RNA secondary structures (hairpins) that form as the nascent RNA emerges from RNA polymerase are important components of many signals that regulate transcription, including some pause sites, all ρ-independent terminators, and some antiterminators. At the his leader pause site, a 5-bp-stem, 8-nt-loop pause RNA hairpin forms 11 nt from the RNA 3′ end and stabilizes a transcription complex conformation slow to react with NTP substrate. This stabilization appears to depend at least in part on an interaction with RNA polymerase. We tested for RNA hairpin interaction with the paused polymerase by crosslinking 5-iodoUMP positioned specifically in the hairpin loop. In the paused conformation, strong and unusual crosslinking of the pause hairpin to β904–950 replaced crosslinking to β′ and to other parts of β that occurred in nonpaused complexes prior to hairpin formation. These changes in nascent RNA interactions may inhibit reactive alignment of the RNA 3′ end in the paused complex and be related to events at ρ-independent terminators.

A role for TFIIH in controlling the activity of early RNA polymerase II elongation complexes

TFIIH is a multifunctional RNA polymerase II transcription factor that possesses DNA-dependent ATPase, DNA helicase, and protein kinase activities. Previous studies have established that TFIIH enters the preinitiation complex and fulfills a critical role in initiation by catalyzing ATP-dependent formation of the open complex prior to synthesis of the first phosphodiester bond of nascent transcripts. In this report, we present direct evidence that TFIIH also controls RNA polymerase II activity at a postinitiation stage of transcription, by preventing premature arrest by very early elongation complexes just prior to their transition to stably elongating complexes. Unexpectedly, we observe that TFIIH is capable of entering the transcription cycle not only during assembly of the preinitiation complex but also after initiation and synthesis of as many as four to six phosphodiester bonds. These findings shed new light on the role of TFIIH in initiation and promoter escape and reveal an unanticipated flexibility in the ability of TFIIH to interact with RNA polymerase II transcription intermediates prior to, during, and immediately after initiation.

Parallel-up structure evidences the molecular directionality during biosynthesis of bacterial cellulose

The “parallel-up” packing in cellulose Iα and Iβ unit cells was experimentally demonstrated by a combination of direct-staining the reducing ends of cellulose chains and microdiffraction-tilting electron crystallographic analysis. Microdiffraction investigation of nascent bacterial cellulose microfibrils showed that the reducing end of the growing cellulose chains points away from the bacterium, and this provides direct evidence that polymerization by the cellulose synthase takes place at the nonreducing end of the growing cellulose chains. This mechanism is likely to be valid also for a number of processive glycosyltransferases such as chitin synthases, hyaluronan synthases, and proteins involved in the synthesis of nodulation factor backbones.

Evidence for protein X binding to a discontinuous epitope on the cellular prion protein during scrapie prion propagation

Studies on the transmission of human (Hu) prions to transgenic (Tg) mice suggested that another molecule provisionally designated protein X participates in the formation of nascent scrapie isoform of prion protein (PrPSc). We report the identification of the site at which protein X binds to the cellular isoform of PrP (PrPC) using scrapie-infected mouse (Mo) neuroblastoma cells transfected with chimeric Hu/MoPrP genes even though protein X has not yet been isolated. Substitution of a Hu residue at position 214 or 218 prevented PrPSc formation. The side chains of these residues protrude from the same surface of the C-terminal α-helix and form a discontinuous epitope with residues 167 and 171 in an adjacent loop. Substitution of a basic residue at positions 167, 171, or 218 also prevented PrPSc formation: at a mechanistic level, these mutant PrPs appear to act as “dominant negatives” by binding protein X and rendering it unavailable for prion propagation. Our findings seem to explain the protective effects of basic polymorphic residues in PrP of humans and sheep and suggest therapeutic and prophylactic approaches to prion diseases.

The α chain of laminin-1 is independently secreted and drives secretion of its β- and γ-chain partners

A mammalian recombinant strategy was established to dissect rules of basement membrane laminin assembly and secretion. The α-, β-, and γ-chain subunits of laminin-1 were expressed in all combinations, transiently and/or stably, in a near-null background. In the absence of its normal partners, the α chain was secreted as intact protein and protein that had been cleaved in the coiled-coil domain. In contrast, the β and γ chains, expressed separately or together, remained intracellular with formation of ββ or βγ, but not γγ, disulfide-linked dimers. Secretion of the β and γ chains required simultaneous expression of all three chains and their assembly into αβγ heterotrimers. Epitope-tagged recombinant α subunit and recombinant laminin were affinity-purified from the conditioned medium of αγ and αβγ clones. Rotary-shadow electron microscopy revealed that the free α subunit is a linear structure containing N-terminal and included globules with a foreshortened long arm, while the trimeric species has the typical four-arm morphology of native laminin. We conclude that the α chain can be delivered to the extracellular environment as a single subunit, whereas the β and γ chains cannot, and that the α chain drives the secretion of the trimeric molecule. Such an α-chain-dependent mechanism could allow for the regulation of laminin export into a nascent basement membrane, and might serve an important role in controlling basement membrane formation.

Cockayne syndrome group B protein enhances elongation by RNA polymerase II

Cockayne syndrome (CS) is characterized by impaired physical and mental development. Two complementation groups, CSA and CSB, have been identified. Here we report that the CSB gene product enhances elongation by RNA polymerase II. CSB stimulated the rate of elongation on an undamaged template by a factor of about 3. A thymine-thymine cyclobutane dimer located in the template strand is known to be a strong block to transcription. Addition of CSB to the blocked polymerase resulted in addition of one nucleotide to the nascent transcript. Finally, addition of transcription factor IIS is known to cause polymerase blocked at a thymine-thymine cyclobutane dimer to digest its nascent transcript, and CSB counteracted this transcript shortening action of transcription factor IIS. Thus a deficiency in transcription elongation may contribute to the CS phenotype.