Unité de Glycobiologie Structurale et Fonctionnelle

factor VIII ◼ pulmonary embolism ◼ thrombosis ◼ von Willebrand factor W e report a case series of patients with coronavirus disease 2019 (CO-VID-19) with pulmonary embolism (PE) in our institution.Lille University Hospital is the tertiary care center for the North of France, the second greatest French region in population density (189 people per 1 km 2 ), also considered a metabolic area with high number of overweight patients.The study was approved by the institutional data protection authority of Lille University Hospital.Among the 107 first consecutive patients with confirmed COVID-19 admitted to the intensive care unit (ICU) for pneumonia from February 27 to March 31, we noticed an unexpectedly high number of PEs during their stay in the ICU: 22 (20.6%) at the time of analysis (April 9), within a median time from ICU admission of 6 days (range, 1-18 days).To determine whether this represents an increase in the expected incidence of PE over a similar time interval, we analyzed the files of 196 patients hospitalized in our ICU during the same time interval in 2019.Despite a similar severity score on admittance to the ICU, the frequency of PE in our CO-VID-19 series was twice as high as the frequency we found in this control period (20.6% versus 6.1%; absolute increased risk, 14.4% [95% CI, 6.1-22.8]).It was also twice as high as the 7.5% frequency of PE in the 40 patients with influenza admitted to the ICU between January 1 and December 30, 2019 (3 PEs; absolute increased risk, 13.1% [95% CI, 1.9-24.3]).A qualitative description of the main characteristics of the patients with PE in the different periods is given in the Table .Taking into account the ICU duration at time of analysis, we estimated the cumulative incidence of PE using the Kalbfleisch and Prentice method by taking into account death (n=15) and discharged alive (n=48) as competing events.The 22 patients still hospitalized in the ICU without PE at the time of analysis (median ICU length of stay, 15 days; range, 10-30 days) were treated as censored observations.At day 15 of ICU admission, the cumulative incidence of PE in patients with COVID-19 in the ICU was estimated to be 20.4% (95% CI, 13.1-28.7).In terms of the main data at ICU admission (using the univariable Fine and Gray model to estimate subhazard ratios of PE), D-dimers (estimate subhazard ratio per log-SD increase, 1.81 [95% CI,1.03-3.16]),plasma factor VIII activity (estimate subhazard ratio per log-SD increase,1.73 [95% CI, 1.10-2.72]),and von Willebrand factor antigen (estimate subhazard ratio per log-SD increase,1.69[95% CI, 1.12-2.56])values seem to be associated with a greater PE risk.At the time of PE diagnosis, 20 of 22 patients were receiving prophylactic antithrombotic treatment (unfractionated heparin or low-molecular-weight heparin) according to the current guidelines in critically ill patients. 1,2One patient with a history of deep venous thrombosis was receiving fluindione with an international normalized ratio in the therapeutic range, and 1 patient was receiving therapeutic unfractionated heparin because of atrial fibrillation.

BACKGROUND: The intestinal mucus layer plays a key role in the maintenance of host-microbiota homeostasis. To document the crosstalk between the host and microbiota, we used gnotobiotic models to study the influence of two major commensal bacteria, Bacteroides thetaiotaomicron and Faecalibacterium prausnitzii, on this intestinal mucus layer. B. thetaiotaomicron is known to use polysaccharides from mucus, but its effect on goblet cells has not been addressed so far. F. prausnitzii is of particular physiological importance because it can be considered as a sensor and a marker of human health. We determined whether B. thetaiotaomicron affected goblet cell differentiation, mucin synthesis and glycosylation in the colonic epithelium. We then investigated how F. prausnitzii influenced the colonic epithelial responses to B. thetaiotaomicron. RESULTS: B. thetaiotaomicron, an acetate producer, increased goblet cell differentiation, expression of mucus-related genes and the ratio of sialylated to sulfated mucins in mono-associated rats. B. thetaiotaomicron, therefore, stimulates the secretory lineage, favoring mucus production. When B. thetaiotaomicron was associated with F. prausnitzii, an acetate consumer and a butyrate producer, the effects on goblet cells and mucin glycosylation were diminished. F. prausnitzii, by attenuating the effects of B. thetaiotaomicron on mucus, may help the epithelium to maintain appropriate proportions of different cell types of the secretory lineage. Using a mucus-producing cell line, we showed that acetate up-regulated KLF4, a transcription factor involved in goblet cell differentiation. CONCLUSIONS: B. thetaiotaomicron and F. prausnitzii, which are metabolically complementary, modulate, in vivo, the intestinal mucus barrier by modifying goblet cells and mucin glycosylation. Our study reveals the importance of the balance between two main commensal bacteria in maintaining colonic epithelial homeostasis via their respective effects on mucus.

Research Article| September 01, 1977 Late Paleozoic strike-slip faulting in southern Europe and northern Africa: Result of a right-lateral shear zone between the Appalachians and the Urals FRANCOIS ARTHAUD; FRANCOIS ARTHAUD 1Laboratoire de Geologie Structural, Universite des Sciences et Techniques du Languedoc, Place E. Bataillon, 34060 Montpellier-Cedex, France Search for other works by this author on: GSW Google Scholar PHILIPPE MATTE PHILIPPE MATTE 1Laboratoire de Geologie Structural, Universite des Sciences et Techniques du Languedoc, Place E. Bataillon, 34060 Montpellier-Cedex, France Search for other works by this author on: GSW Google Scholar Author and Article Information FRANCOIS ARTHAUD 1Laboratoire de Geologie Structural, Universite des Sciences et Techniques du Languedoc, Place E. Bataillon, 34060 Montpellier-Cedex, France PHILIPPE MATTE 1Laboratoire de Geologie Structural, Universite des Sciences et Techniques du Languedoc, Place E. Bataillon, 34060 Montpellier-Cedex, France Publisher: Geological Society of America First Online: 01 Jun 2017 Online ISSN: 1943-2674 Print ISSN: 0016-7606 Geological Society of America GSA Bulletin (1977) 88 (9): 1305–1320. https://doi.org/10.1130/0016-7606(1977)88<1305:LPSFIS>2.0.CO;2 Article history First Online: 01 Jun 2017 Cite View This Citation Add to Citation Manager Share Icon Share Facebook Twitter LinkedIn Email Permissions Search Site Citation FRANCOIS ARTHAUD, PHILIPPE MATTE; Late Paleozoic strike-slip faulting in southern Europe and northern Africa: Result of a right-lateral shear zone between the Appalachians and the Urals. GSA Bulletin 1977;; 88 (9): 1305–1320. doi: https://doi.org/10.1130/0016-7606(1977)88<1305:LPSFIS>2.0.CO;2 Download citation file: Ris (Zotero) Refmanager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentBy SocietyGSA Bulletin Search Advanced Search Abstract Late Paleozoic wrench faulting in southern Europe and northern Africa is interpreted as a right-lateral shear zone induced by the relative motion of two plates – a northern one that includes the Canadian Shield, Greenland, and stable Europe and a southern one that includes the African Shield plus an unknown eastern extension. The relative movement of these two plates was transformed into shortening at both ends of the shear zone and led to the formation of late Paleozoic mountain belts: the Urals to the east and the southern Appalachians to the west. Theoretical and experimental models of the dynamics of faulting may account for the arrangement of the fractures in the shear zone and for the observed displacements. This content is PDF only. Please click on the PDF icon to access. First Page Preview Close Modal You do not have access to this content, please speak to your institutional administrator if you feel you should have access.

Microtubules (MTs) play a fundamental role in many vital processes such as cell division and neuronal activity. They are key structural and functional elements in axons, supporting neurite differentiation and growth, as well as transporting motor proteins along the axons, which use MTs as support tracks. Tau is a stabilizing MT associated protein, whose functions are mainly regulated by phosphorylation. A disruption of the MT network, which might be caused by Tau loss of function, is observed in a group of related diseases called tauopathies, which includes Alzheimer's disease (AD). Tau is found hyperphosphorylated in AD, which might account for its loss of MT stabilizing capacity. Since destabilization of MTs after dissociation of Tau could contribute to toxicity in neurodegenerative diseases, a molecular understanding of this interaction and its regulation is essential.

Successful treatment of human tuberculosis requires 6-9 months' therapy with multiple antibiotics. Incomplete clearance of tubercle bacilli frequently results in disease relapse, presumably as a result of reactivation of persistent drug-tolerant Mycobacterium tuberculosis cells, although the nature and location of these persisters are not known. In other pathogens, antibiotic tolerance is often associated with the formation of biofilms--organized communities of surface-attached cells--but physiologically and genetically defined M. tuberculosis biofilms have not been described. Here, we show that M. tuberculosis forms biofilms with specific environmental and genetic requirements distinct from those for planktonic growth, which contain an extracellular matrix rich in free mycolic acids, and harbour an important drug-tolerant population that persist despite exposure to high levels of antibiotics.

Plant starch granules provide the largest percentage of calories in the human diet. Starch consists almost entirely of the Glc homopolymers amylopectin and amylose. Amylopectin is the major contributor to both mass and granule structure. Because of the very basic role that starch plays in our society, increased understanding of the biosynthetic mechanisms that produce amylopectin is important. Amylopectin is an important industrial raw material, and much remains to be determined about the relations between its biosynthesis and functionality. It is also a fascinating molecule in its own right, because it exhibits a high degree of architectural specificity despite containing only one type of monomeric unit (i.e. the glucosyl group) connected via just two linkage types. Thus, significant insights into basic biochemical mechanisms may be obtained by studying amylopectin biosynthesis. Amylopectin is chemically similar to glycogen in that both are α(1→4)-linked, α(1→6)-branched Glc homopolymers, although a major difference between them is the organization of the latter into large, insoluble, semicrystalline granules. Polysaccharides of this type synthesized in vitro do not readily crystallize, which is indicative of the relation between amylopectin biosynthesis and granule formation. In this Update we address the biological mechanisms underlying amylopectin crystallization, in particular those steps that could distinguish the amylopectin pathway in plants from the glycogen pathway in a presumptive cyanobacterial ancestor. The enzymes to be discussed include starch synthases (SSs) and starch branching enzymes (BEs), both of which are involved directly in amylopectin biosynthesis. In addition, we discuss two enzymes for which potential roles in amylopectin biosynthesis are suggested by genetic data, namely starch debranching enzymes (DBEs) and disproportionating enzyme (D-enzyme). Other important aspects of amylopectin biosynthesis that are outside the scope of this Update include production of the glucosyl unit donor ADPGlc, amylose biosynthesis (Ball et al., 1998), polymer chain initiation, and granule initiation. Diagrammatic representation of the proposed first three levels of amylopectin (Ap) structure (adapted from Gallant et al., 1997). A, Connection of glucosyl units via α(1→4) and α(1→6) glycoside linkages. The specific chain organization shown is not intended to illustrate the actual structure of amylopectin. B, Cluster model of amylopectin structure. Solid lines indicate glucan chains, and intersections between them indicate branch linkages. Dotted lines indicate the boundaries of amylopectin side chain clusters in which primarily unbranched chains associate in tightly packed double helices. a, Amorphous areas that separate amylopectin side chain clusters. C, Diagrammatic representation of a blocklet, which is made up of amylopectin side chain clusters organized into a discrete unit. Amylopectin exhibits hierarchical levels of specific architectural structure. At the 0.1- to 1.0-nm scale, i.e. within individual chains, structure is described by branch location and chain length. Amylopectin can be completely converted into linear chains by enzymatic cleavage of all branch linkages, and the frequency of chains of specific length can then be quantified (Morell et al., 1998, and refs. therein). Such data reveal non-random chain length distributions generally conserved in amylopectin from different plants. Other studies involving enzymatic treatment prior to determination of residual chain length distribution provide estimates of the distances between branch points. This parameter also is non-random, indicating that branches are clustered. Thus, to understand the amylopectin biosynthetic mechanism, it is necessary to know what determines the specific lengths of A and B chains and how the non-random location of branch linkages along B chains is attained. The next structural level occurs on the 10-nm scale (Fig. 1B). Regions called crystalline lamellae, recognizable by their resistance to acid hydrolysis, are thought to comprise tightly associated double helices containing primarily A chains and unsubstituted spans of B chains. Crystalline lamellae alternate with regions susceptible to acid hydrolysis called amorphous lamellae, which are thought to contain frequent branch linkages and thus be less densely packed. The 9- to 10-nm thickness of the repeating unit of crystalline and amorphous lamellae is generally conserved in the plant kingdom (Jenkins et al., 1993). Crystalline lamellae are thought to be divided into discrete units about 10-nm wide called amylopectin side chain clusters (Gallant et al., 1997). Clustering of branches in the lowest order structure is thought to allow organization of the subsequent level, because regions of relatively low branch frequency are necessary for amylopectin side chain clusters to form. Specific chain length distributions and arrangements may also be required for side chain cluster formation to be energetically favorable. The next level of structure, on the 100-nm scale, is proposed to be the blocklet (Gallant et al., 1997). Crystalline and amorphous lamellae were seen by transmission electron microscopy to be grouped into discrete, elongated structures surrounded by relatively large, non-crystalline regions (Fig. 1C). Areas between blocklets are about 10 to 20 nm wide, compared with 3 to 4 nm for amorphous lamellae. Blocklets within a granule vary in size and shape, but can be approximated as oblate spheroids with short diameters of 20 to 500 nm. Blocklets are believed to be aligned relative to each other in various ways, rather than having a common orientation. The next structural level within starch granules is observed as characteristic alternating rings ranging in thickness from 120 to 500 nm. These distinct, alternating rings are called crystalline shells and semicrystalline shells. Different shells may each consist of distinct types of blocklets that vary in size and/or packing geometry. Considering their dimensions, two or three layers of blocklets could make up a shell. Further considerations of starch granule structure involve packing of amylose and other components such as lipids into the framework established by amylopectin. Amylopectin biosynthesis must be examined within the framework of the overall hierarchical structure of the product. Although the basic enzymatic steps are relatively well understood, much remains to be learned about the relationship between enzyme action and amylopectin structure. The SSs, BEs, and, potentially, DBEs and D-enzymes, will determine the fundamental structure of the molecule, e.g. A chain length and the placement of branches along B chains. At some point the glucans produced by the enzyme system must assume higher order structures, although neither how nor when this occurs is known. For example, in a minimalist model it is possible that each A chain as it is synthesized is packaged immediately into a side chain cluster. Alternatively, clusters might not form until all of the constituent chains have been formed. Extending the latter suggestion to the other extreme, entire amylopectin molecules may be packaged all at once into amylopectin side chain clusters, alternating crystalline and amorphous lamellae, blocklets, and crystalline or semicrystalline shells. Thus, it is necessary to understand not only the particular activity of each enzyme, but also the relationship between the synthesis of the primary product and subsequent packing into higher order structures. Consideration of amylopectin structure highlights an inherent difficulty in analyzing these biosynthetic enzymes, which is that their native substrates are not defined. SSs, BEs, and other potential biosynthetic enzymes act within plastids on glucans likely to be very different in terms of concentration, secondary structure, and tertiary arrangement than artificial substrates used in vitro. Any in vitro enzyme characterization must be interpreted relative to actual cellular conditions, and this consideration is particularly important regarding amylopectin biosynthesis. General pathway of starch biosynthesis beginning with Suc as the product of photosynthesis. Activities are as follows. 1, Suc synthase; 2, UDP-Glc pyrophosphorylase; 3, glycolytic enzymes including phosphoglucomutase; 4, ADPGlc pyrophosphorylase; 5, hexose phosphate transporters; 6, ADPGlc transporters. Not all plants possess both the indicated transporters and cytosolic ADPGlc pyrophosphorylase. Transport of Glc-1-P is depicted as a possible example and is not meant to imply that hexose phosphate transporters are necessarily specific for this molecule. Ap, Amylopectin; Am, amylose. Diagrammatic representation of the chemical reactions catalyzed by enzymes involved in amylopectin biosynthesis. Donated glucosyl units are shown in red, and asterisks indicate reducing carbons through which these glucans are transferred. Structures are shown only to illustrate changes in linkage structure and are not intended to indicate substrate specificities. The GBSSI, SSI, SSII, and SSIII isoforms are conserved broadly in evolution, suggesting that specific functions have been selected. Mutational and antisense analyses support this hypothesis, because interference with a specific isoform often results in structural alterations in amylopectin (Edwards et al., 1999; Lloyd et al., 1999, and refs. therein). Thus, in some instances, SSs do not substitute fully for one another. Details about the distinct enzymatic properties of SS isoforms are emerging through characterization of purified native or recombinant enzymes (Imparl-Radosevich et al., 1999, and refs. therein). Considering, however, that the native primers are not characterized and that isoform specificities overlap to varying degrees, it remains difficult to define individual SS functions. Isoform specificities, e.g. with respect to chain length, action in the proximity of branch points, and relative action on freely soluble versus granule-associated glucans, thus remain a challenging subject for research. BEs also are present as multiple isoforms. BEs catalyze the cleavage of α(1→4) linkages and transfer of the released reducing end to a C6 hydroxyl, creating a new α(1→6) linkage (Fig. 3). Two classes are known from specific sequence conservation patterns (Smith et al., 1997). Two nomenclatures have evolved in which one class is known as BEI in maize or B in pea, and the other class as BEII in maize or A in pea. In maize, the BEII class contains two genetically distinct members, BEIIa and BEIIb. Pea embryos, potato tubers, and endosperm of maize, wheat, barley, and rice all possess both classes. There have been efforts to characterize the differing specificities of branching enzymes, but much remains to be learned. Analysis of recombinant maize enzymes revealed that with amylose as the substrate, BEI transfers longer chains than BEIIb (Guan and Preiss, 1993). Substrate preference in vitro also varied, with BEI being more active toward amylose and BEIIb preferring amylopectin. Similar results were obtained with purified wheat BEs (Morell et al., 1997). Defining the specificity of individual BEs is complex and will involve consideration not only of the chain lengths transferred, but also definition of the reaction rates with respect to cleavage distance from a reducing end, a non-reducing end, or a branch linkage. Specificity may also be expected regarding proximity of the acceptor site, i.e. the newly formed branch, to these chemical reference points. There has been little comprehensive work to define these parameters. Whether SSs and BEs can produce a glucan able to auto-assemble into semicrystalline amylopectin is not yet known. the of an amylopectin biosynthetic system with specific In one to produce maize BEI and BEIIb in the (Guan et al., The produced in with the glucan were distinct from amylopectin and the relatively molecule The are not likely to entirely determine the higher order structures of amylopectin. including multiple isoforms of SS and at the might produce glucan some hierarchical structures of e.g. side chain clusters or Such results allow regarding which enzymes are required for synthesis of the amylopectin A to for amylopectin the specific of an enzyme, although do a of that must be as possible of amylopectin structure. DBEs catalyze the hydrolysis of α(1→6) linkages (Fig. 3). multiple isoforms are to as DBEs and and structural distinguish the et al., 1999, and refs. therein). DBEs α(1→6) linkages in and (i.e. but do not branches in a polymer of repeating DBEs called or in that readily and but are less active or toward glycogen and amylopectin. The biochemical of both isoforms has been described plant DBEs are with of to 500 for both the potato and rice endosperm enzymes et al., et al., This to the size generally conserved in as shown by of of and were from the purified complex of although these have not been In the purified rice only a by revealed two in the although and that from the or from two very et al., obtained from recombinant maize purified from which is with a structure et al., The that some may contain two or more be however, that multiple are in and that at some possess for two DBEs DBEs as although the with the isoform that a can in multiple that vary by et al., et al., et al., et al., 1999, and refs. therein). Amylopectin not to levels when an is suggesting that this enzyme in starch biosynthesis. The maize starch biosynthesis in endosperm and and for an et al., et al., The for an and starch from to levels et al., of the an and also a in starch biosynthesis et al., the rice for an and similar in starch production et al., et al., These provide that interference with DBEs the of amylopectin biosynthesis. from genetic are by potential i.e. one may multiple This is the in maize and because both the and the isoforms are et al., et al., In and however, the only is in the These results that branch linkage hydrolysis is required for amylopectin In all the of the amylopectin is by the and the and frequency in is about that in amylopectin. not the higher order structures of because the chain length distribution is toward linear and B chains with multiple branches are and amylopectin in maize, and et al., et al., its concentration, the structure of the residual amylopectin in to be et al., In and rice plants a specific is a of amylopectin et al., et al., 1997). is soluble and thus separate from amylopectin in granules. glucans in the however, as shown by microscopy of and maize endosperm and et al., In rice are regions of the endosperm that to granules or distinct from other areas containing amylopectin et al., 1997). The data indicate that DBEs are not then glucosyl units for into amylopectin are into a more molecule. understand this it is first necessary to determine is the of the biosynthetic The that the is for of a different enzyme, and that this in amylopectin DBEs are for amylopectin then a is act directly along with SSs and or in a distinct pathway that amylopectin biosynthesis Because of the specific of the and we the that is by the not from changes in This is by the that all known at one were then other types of be to The that DBEs in amylopectin biosynthesis that are conserved in plants and at the of glucan formation. are by DBEs are conserved in and indicating a these enzymes also in including endosperm of maize, and barley, and et al., et al., et al., 1999; et al., are indicated in maize and by in the and rice and by an DBEs were indicating that likely have to amylopectin its DBEs also to be broadly with in This isoform has been in maize, and et al., 1999; et al., 1999, and refs. therein). location of DBEs starch biosynthesis in maize endosperm et al., and et al., that and DBEs of the plant and that each has been for DBEs are known from rice maize and et al., 1999; et al., 1999, and refs. therein). are known in maize, barley, wheat, and two distinct et al., et al., et al., 1999; et al., The isoforms compared different are to the two isoforms within a is less than that observed when enzyme is compared with a or Thus, and DBEs are likely to functions in glucan also as a potential in amylopectin biosynthesis. transfer a of one linear chain to (Fig. 3). α(1→4) linkage is and the released reducing end is to a separate chain through a new α(1→4) linkage. of the of a on other known starch biosynthetic enzymes et al., amylopectin when is and its structure is by a significant in the frequency of short A chains. in the soluble from the In to the made for may an amylopectin or in a separate pathway required for amylopectin biosynthesis. The of in amylopectin biosynthesis may vary on or The were observed only in of not in and starch at much higher changes in starch biosynthesis in potato an antisense et al., Thus, it remains to be determined are generally involved in amylopectin and in this it will be to to in other the proposed of in amylopectin biosynthesis not a in starch are known from of pea, and potato tubers, and et al., In or entirely within the and in potato the is in as starch is plant are known only from potato and an and these two are less than proposed to in amylopectin (Ap) biosynthesis. for and The and the in indicate the in the of SSs and BEs more into and less amylopectin. The glucosyl units in produced by action the of are to the beginning of the on in maize of a called branching enzyme, which able to amylose into 1997). branching enzyme to be from maize, the of only (Fig. In subsequent however, similar activity were purified from endosperm of both and maize and rice and Preiss, et al., a to has not yet been studies in maize revealed that is or in double and Thus, the product of is for and this enzyme functions in plants. that maize and and for DBEs is difficult to with the production of a in the these the remains that activity in is as a secondary of a The that maize for an and that in this isoform starch completely the of an that is an in amylopectin biosynthesis (Ball et al., to the branches are from a called it to amylopectin (Fig. The substrate specificity of the maize that in it may branches more readily than those the distribution of and unbranched areas required for the formation of amylopectin side chain clusters. A of involving by SSs, branching by BEs, debranching by and the formation of crystalline lamellae has been SS action on non-reducing then the A different to as the proposed to the that and starch granules with amylopectin in the et al., This is to the because in that amylopectin form to the DBEs the of a pathway in the soluble (Fig. SSs and BEs are proposed to work both in with granules and in the the latter pathway on to produce glucans to as DBEs in the of thus the of SSs and BEs from their action at the granule In this synthesis with amylopectin and DBEs that the amylopectin pathway the be less able to glucan synthesis in the that along with amylopectin and the of the latter is The model involving amylopectin (Ap) as a The a of glucans that are by the indicated Thus, the molecules as a of structures. is proposed to be released by is proposed to transfer linear chains from directly into and also to in the of ADPGlc from Not indicated is the that may as a for The that also the transfer of glucans chains in is also is proposed to from the and make it to enzymatic The that in the of can be by SSs and BEs to the point is not for the synthesis of amylopectin molecules is substrates for SSs, BEs, and a lowest order structure for is and then into a higher order structure packing within regions is proposed to to biosynthetic glucan is into amylopectin. In this is as glucan to the amylopectin is as the that occurs to the higher order structures. It is how the to must be to allow to amylopectin. is proposed to be required for to a structure, and this could not a level of In this remain in the soluble to SSs, BEs, and other enzymes, The of amylopectin with observed in might be by this activity is but not then may at a than because of the longer to a structure for on remain to enzymatic for an This action might the into a form for which is longer it into the between and be a on the and/or specificity of and both amylopectin and form This could the of both starch and in some activity may be only in these because of the of isoforms of the or The model must also and amylopectin form in separate i.e. the soluble and starch It is possible that the between amylopectin and occurs very in the synthesis of one molecule. may at a very level, as as a amylopectin side chain cluster. This may provide an for the of regions into the crystalline structure. this is by structural from then may because of SS and Thus, molecules may separate very in their synthesis from those to be converted into is that on the of the molecules both crystalline regions into the granule and regions in the soluble These two areas might be by or by a of this it will be to characterize the glucans formed in plants that The of multiple and/or can be to such plants. of amylopectin are then it that DBEs to a the that amylopectin is completely in plants that synthesis is the pathway of amylopectin and also that the of glucosyl units from into amylopectin synthesis is on The characterization of that may also to the glucosyl units from into amylopectin biosynthesis may involve enzymes other than e.g. enzymes involved in Such functions might be which could provide support for the potential of the is to characterize plants with alterations in specificity but not its e.g. by enzymes from other or the relative levels of the native isoforms. The of might less substrate specificity than the of the of specificity with overall activity levels might provide support for one of these The between in and structural changes in amylopectin a potential biosynthetic role for this may a role in amylopectin or it could be involved in of glucosyl units from or into amylopectin biosynthesis. It is likely that DBEs prior to the of as the This is with the role of DBEs as proposed in the model or the Two have been proposed for the role of in amylopectin may as it in for such that the enzyme to Glc and other chains and The latter be substrates for and thus be converted to and Glc could be by a hexose The glucosyl units then be to ADPGlc and the biosynthetic via This model could for the in amylopectin biosynthesis that with although it not the chain lengths observed in amylopectin A is that directly transfers glucan chains from produced by DBEs into the A chains of amylopectin. This model could both the in amylopectin biosynthesis and the chain length This is because the transfer of glucosyl units from directly into amylopectin has been in vitro. is that donor and acceptor chains both into amylopectin. Thus, be in to SS and as a potential of chain length distribution (Fig. The complex of starch biosynthesis because of its and its in starch produced in plastids with glycogen in that the biosynthetic pathway has in because of a semicrystalline product. This plants to of by photosynthesis. The to amylopectin biosynthesis could have evolved through in the branching enzymes and glucan synthases involved in glycogen Alternatively, glycogen biosynthesis may have been to produce amylopectin through the of the functions of enzymes to glucan structure that is The of enzymes might be a then complex branching enzymes and glucan synthases of a This of enzymes into a biosynthetic pathway may be a common because both and DBEs have been in this genetic is to determine other enzymes thought to have roles might also to amylopectin biosynthesis. however, the of amylopectin biosynthesis as the of complex and alterations involving both SS and as well as of DBEs and into some aspects of the These studies on a polymer such as which in a high degree of hierarchical structure, are likely to be to those to understand more hierarchical structures such as the plant or

Background The association of pulmonary embolism (PE) with deep vein thrombosis (DVT) in patients with coronavirus disease 2019 (COVID-19) remains unclear, and the diagnostic accuracy of D-dimer tests for PE is unknown. Purpose To conduct meta-analysis of the study-level incidence of PE and DVT and to evaluate the diagnostic accuracy of D-dimer tests for PE from multicenter individual patient data. Materials and Methods A systematic literature search identified studies evaluating the incidence of PE or DVT in patients with COVID-19 from January 1, 2020, to June 15, 2020. These outcomes were pooled using a random-effects model and were further evaluated using metaregression analysis. The diagnostic accuracy of D-dimer tests for PE was estimated on the basis of individual patient data using the summary receiver operating characteristic curve. Results Twenty-seven studies with 3342 patients with COVID-19 were included in the analysis. The pooled incidence rates of PE and DVT were 16.5% (95% CI: 11.6, 22.9; I2 = 0.93) and 14.8% (95% CI: 8.5, 24.5; I2 = 0.94), respectively. PE was more frequently found in patients who were admitted to the intensive care unit (ICU) (24.7% [95% CI: 18.6, 32.1] vs 10.5% [95% CI: 5.1, 20.2] in those not admitted to the ICU) and in studies with universal screening using CT pulmonary angiography. DVT was present in 42.4% of patients with PE. D-dimer tests had an area under the receiver operating characteristic curve of 0.737 for PE, and D-dimer levels of 500 and 1000 μg/L showed high sensitivity (96% and 91%, respectively) but low specificity (10% and 24%, respectively). Conclusion Pulmonary embolism (PE) and deep vein thrombosis (DVT) occurred in 16.5% and 14.8% of patients with coronavirus disease 2019 (COVID-19), respectively, and more than half of patients with PE lacked DVT. The cutoffs of D-dimer levels used to exclude PE in preexisting guidelines seem applicable to patients with COVID-19. © RSNA, 2020 Supplemental material is available for this article. See also the editorial by Woodard in this issue.

Cryptophyte and chlorarachniophyte algae are transitional forms in the widespread secondary endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae. Unlike most secondary plastid-bearing algae, miniaturized versions of the endosymbiont nuclei (nucleomorphs) persist in cryptophytes and chlorarachniophytes. To determine why, and to address other fundamental questions about eukaryote–eukaryote endosymbiosis, we sequenced the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. Both genomes have >21,000 protein genes and are intron rich, and B. natans exhibits unprecedented alternative splicing for a single-celled organism. Phylogenomic analyses and subcellular targeting predictions reveal extensive genetic and biochemical mosaicism, with both host- and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosymbiont cytosol of both algae. Mitochondrion-to-nucleus gene transfer still occurs in both organisms but plastid-to-nucleus and nucleomorph-to-nucleus transfers do not, which explains why a small residue of essential genes remains locked in each nucleomorph. Sequencing the nuclear genomes of Guillardia theta and Bigelowiella natans, transitional forms in the endosymbiotic acquisition of photosynthesis by engulfment of certain eukaryotic algae, reveals unprecedented alternative splicing for a single-celled organism (B. natans) and extensive genetic and biochemical mosaicism, shedding light on why nucleomorphs persist in these species but not other algae. This paper presents the sequences of the nuclear genomes of two eukaryotic microbes of remarkable genetic and cellular complexity, Guillardia and Bigelowiella. These algae are transitional forms in the endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae, and possess four genomes: mitochondrial and plastid (chloroplast) genomes, a nuclear genome of host origin and a miniaturized 'nucleomorph' genome of endosymbiotic origin. Analyses reveal unprecedented alternative splicing for a single-celled organism, and extensive genetic and biochemical mosaicism. Whereas the mitochondrion-to-nucleus gene transfer continues in both organisms, plastid-to-nucleus and nucleomorph-to-nucleus transfers have ceased, explaining nucleomorph persistence.

The phenylpropanoid pathway in plants is responsible for the biosynthesis of a huge amount of secondary metabolites derived from phenylalanine and tyrosine. Both flavonoids and lignins are synthesized at the end of this very diverse metabolic pathway, as well as many intermediate molecules whose precise biological functions remain largely unknown. The diversity of these molecules can be further increased under the action of UDP-glycosyltransferases (UGTs) leading to the production of glycosylated hydroxycinnamates and related aldehydes, alcohols and esters. Glycosylation can change phenylpropanoid solubility, stability and toxic potential, as well as influencing compartmentalization and biological activity. (De)-glycosylation therefore represents an extremely important regulation point in phenylpropanoid homeostasis. In this article we review recent knowledge on the enzymes involved in regulating phenylpropanoid glycosylation status and availability in different subcellular compartments. We also examine the potential link between monolignol glycosylation and lignification by exploring co-expression of lignin biosynthesis genes and phenolic (de)glycosylation genes. Of the different biological roles linked with their particular chemical properties, phenylpropanoids are often correlated with the plant's stress management strategies that are also regulated by glycosylation. UGTs can for instance influence the resistance of plants during infection by microorganisms and be involved in the mechanisms related to environmental changes. The impact of flavonoid glycosylation on the color of flowers, leaves, seeds and fruits will also be discussed. Altogether this paper underlies the fact that glycosylation and deglycosylation are powerful mechanisms allowing plants to regulate phenylpropanoid localisation, availability and biological activity.

Purified human mucins from different parts of the intestinal tract (ileum, cecum, transverse and sigmoid colon and rectum) were isolated from two individuals with blood group ALe(b) (A-Lewis(b)). After alkaline borohydride treatment the released oligosaccharides were structurally characterized by nano-ESI Q-TOF MS/MS (electrospray ionization quadrupole time-of-flight tandem MS) without prior fractionation or derivatization. More than 100 different oligosaccharides, with up to ten monosaccharide residues, were identified using this technique. Oligosaccharides based on core 3 structures, GlcNAc(beta1-3)GalNAc (where GlcNAc is N-acetyl-D-glucosamine and GalNAc is N-acetylgalactosamine), were widely distributed in human intestinal mucins. Core 5 structures, GalNAc(alpha1-3)GalNAc, were also recovered in all fractions. Moreover, a comparison of the oligosaccharide repertoire, with respect to size, diversity and expression of glycans and terminal epitopes, showed a high level of mucin-specific glycosylation: highly fucosylated glycans, found specifically in the small intestine, were mainly based on core 4 structures, GlcNAc-(beta1-3)[GlcNAc(beta1-6)]GalNAc, whereas the sulpho-Le(X) determinant carrying core 2 glycans, Gal(beta1-3)[GlcNAc(beta1-6)]-GalNAc (where Gal is galactose), was recovered mainly in the distal colon. Blood group H and A antigenic determinants were present exclusively in the ileum and cecum, whereas blood group Sd(a)/Cad related epitopes, GalNAc(beta1-4)[NeuAc(alpha2-3)]Gal (where NeuAc is N-acetylneuraminate), were found to increase along the length of the colon. Our findings suggest that mucins create an enormous repertoire of potential binding sites for micro-organisms that could explain the regio-specific colonization of bacteria in the human intestinal tract.

Red seaweeds are key components of coastal ecosystems and are economically important as food and as a source of gelling agents, but their genes and genomes have received little attention. Here we report the sequencing of the 105-Mbp genome of the florideophyte Chondrus crispus (Irish moss) and the annotation of the 9,606 genes. The genome features an unusual structure characterized by gene-dense regions surrounded by repeat-rich regions dominated by transposable elements. Despite its fairly large size, this genome shows features typical of compact genomes, e.g., on average only 0.3 introns per gene, short introns, low median distance between genes, small gene families, and no indication of large-scale genome duplication. The genome also gives insights into the metabolism of marine red algae and adaptations to the marine environment, including genes related to halogen metabolism, oxylipins, and multicellularity (microRNA processing and transcription factors). Particularly interesting are features related to carbohydrate metabolism, which include a minimalistic gene set for starch biosynthesis, the presence of cellulose synthases acquired before the primary endosymbiosis showing the polyphyly of cellulose synthesis in Archaeplastida, and cellulases absent in terrestrial plants as well as the occurrence of a mannosylglycerate synthase potentially originating from a marine bacterium. To explain the observations on genome structure and gene content, we propose an evolutionary scenario involving an ancestral red alga that was driven by early ecological forces to lose genes, introns, and intergenetic DNA; this loss was followed by an expansion of genome size as a consequence of activity of transposable elements.

Plastid Origins The glaucophytes, represented by the alga Cyanophora paradoxa , are the putative sister group of red and green algae and plants, which together comprise the founding group of photosynthetic eukaryotes, the Plantae. In their analysis of the genome of C. paradoxa , Price et al. (p. 843 ; see the Perspective by Spiegel ) demonstrate a unique origin for the plastid in the ancestor of this supergroup, which retains much of the ancestral diversity in genes involved in carbohydrate metabolism and fermentation, as well as in the gene content of the mitochondrial genome. Moreover, about 3.3% of nuclear genes in C. paradoxa seem to carry a signal of cyanobacterial ancestry, and key genes involved in starch biosynthesis are derived from energy parasites such as Chlamydiae. Rapid radiation, reticulate evolution via horizontal gene transfer, high rates of gene divergence, loss, and replacement, may have diffused the evolutionary signals within this supergroup, which perhaps explains previous difficulties in resolving its evolutionary history.

The imprinted H19 gene has riboregulatory functions. We show here that H19 transcription is up-regulated during the S-phase of growth-stimulated cells and that the H19 promoter is activated by E2F1 in breast cancer cells. H19 repression by pRb and E2F6 confirms the E2F1-dependent control of the H19 promoter. Consistently, we demonstrate by chromatin immunoprecipitation assays that endogenous E2F1 is recruited to the H19 promoter in vivo. The functionality of E2F promoter sites was further confirmed by gel shift and mutagenesis experiments, revealing that these sites are required for binding and promoter response to E2F1 exogenous expression and serum stimulation. Furthermore, we show that H19 overexpression confers a growth advantage on breast cancer cells released from growth arrest as well as in asynchronously growing cells. The H19 knockdown by small interfering RNA duplexes impedes S-phase entry in both wild-type and stably H19-transfected cells. Based on these findings, we conclude that the H19 RNA is actively linked to E2F1 to promote cell cycle progression of breast cancer cells. This clearly supports the H19 oncogenic function in breast tumor genesis.

New molecular modeling approaches, driven by rapidly improving computational platforms, have allowed many success stories for the use of computer-assisted drug design in the discovery of new mechanism-or structure-based drugs. In this overview, we highlight three aspects of the use of molecular docking. First, we discuss the combination of molecular and quantum mechanics to investigate an unusual enzymatic mechanism of a flavoprotein. Second, we present recent advances in anti-infectious agents' synthesis driven by structural insights. At the end, we focus on larger biological complexes made by protein-protein interactions and discuss their relevance in drug design. This review provides information on how these large systems, even in the presence of the solvent, can be investigated with the outlook of drug discovery.

BACKGROUND: The antiviral efficacy of remdesivir against SARS-CoV-2 is still controversial. We aimed to evaluate the clinical efficacy of remdesivir plus standard of care compared with standard of care alone in patients admitted to hospital with COVID-19, with indication of oxygen or ventilator support. METHODS: DisCoVeRy was a phase 3, open-label, adaptive, multicentre, randomised, controlled trial conducted in 48 sites in Europe (France, Belgium, Austria, Portugal, Luxembourg). Adult patients (aged ≥18 years) admitted to hospital with laboratory-confirmed SARS-CoV-2 infection and illness of any duration were eligible if they had clinical evidence of hypoxaemic pneumonia, or required oxygen supplementation. Exclusion criteria included elevated liver enzymes, severe chronic kidney disease, any contraindication to one of the studied treatments or their use in the 29 days before random assignment, or use of ribavirin, as well as pregnancy or breastfeeding. Participants were randomly assigned (1:1:1:1:1) to receive standard of care alone or in combination with remdesivir, lopinavir-ritonavir, lopinavir-ritonavir and interferon beta-1a, or hydroxychloroquine. Randomisation used computer-generated blocks of various sizes; it was stratified on severity of disease at inclusion and on European administrative region. Remdesivir was administered as 200 mg intravenous infusion on day 1, followed by once daily, 1-h infusions of 100 mg up to 9 days, for a total duration of 10 days. It could be stopped after 5 days if the participant was discharged. The primary outcome was the clinical status at day 15 measured by the WHO seven-point ordinal scale, assessed in the intention-to-treat population. Safety was assessed in the modified intention-to-treat population and was one of the secondary outcomes. This trial is registered with the European Clinical Trials Database, EudraCT2020-000936-23, and ClinicalTrials.gov, NCT04315948. FINDINGS: Between March 22, 2020, and Jan 21, 2021, 857 participants were enrolled and randomly assigned to remdesivir plus standard of care (n=429) or standard of care only (n=428). 15 participants were excluded from analysis in the remdesivir group, and ten in the control group. At day 15, the distribution of the WHO ordinal scale was: (1) not hospitalised, no limitations on activities (61 [15%] of 414 in the remdesivir group vs 73 [17%] of 418 in the control group); (2) not hospitalised, limitation on activities (129 [31%] vs 132 [32%]); (3) hospitalised, not requiring supplemental oxygen (50 [12%] vs 29 [7%]); (4) hospitalised, requiring supplemental oxygen (76 [18%] vs 67 [16%]); (5) hospitalised, on non-invasive ventilation or high flow oxygen devices (15 [4%] vs 14 [3%]); (6) hospitalised, on invasive mechanical ventilation or extracorporeal membrane oxygenation (62 [15%] vs 79 [19%]); (7) death (21 [5%] vs 24 [6%]). The difference between treatment groups was not significant (odds ratio 0·98 [95% CI 0·77-1·25]; p=0·85). There was no significant difference in the occurrence of serious adverse events between treatment groups (remdesivir, 135 [33%] of 406 vs control, 130 [31%] of 418; p=0·48). Three deaths (acute respiratory distress syndrome, bacterial infection, and hepatorenal syndrome) were considered related to remdesivir by the investigators, but only one by the sponsor's safety team (hepatorenal syndrome). INTERPRETATION: No clinical benefit was observed from the use of remdesivir in patients who were admitted to hospital for COVID-19, were symptomatic for more than 7 days, and required oxygen support. FUNDING: European Union Commission, French Ministry of Health, Domaine d'intérêt majeur One Health Île-de-France, REACTing, Fonds Erasme-COVID-Université Libre de Bruxelles, Belgian Health Care Knowledge Centre, Austrian Group Medical Tumor, European Regional Development Fund, Portugal Ministry of Health, Portugal Agency for Clinical Research and Biomedical Innovation. TRANSLATION: For the French translation of the abstract see Supplementary Materials section.

We discuss protein post-translational modification (PTM) from an information processing perspective. PTM at multiple sites on a protein creates a combinatorial explosion in the number of potential 'mod-forms', or global patterns of modification. Distinct mod-forms can elicit distinct downstream responses, so that the overall response depends partly on the effectiveness of a particular mod-form to elicit a response and partly on the stoichiometry of that mod-form in the molecular population. We introduce the 'mod-form distribution'-the relative stoichiometries of each mod-form-as the most informative measure of a protein's state. Distinct mod-form distributions may summarize information about distinct cellular and physiological conditions and allow downstream processes to interpret this information accordingly. Such information 'encoding' by PTMs may facilitate evolution by weakening the need to directly link upstream conditions to downstream responses. Mod-form distributions provide a quantitative framework in which to interpret ideas of 'PTM codes' that are emerging in several areas of biology, as we show by reviewing examples of ion channels, GPCRs, microtubules, and transcriptional co-regulators. We focus particularly on examples other than the well-known 'histone code', to emphasize the pervasive use of information encoding in molecular biology. Finally, we touch briefly on new methods for measuring mod-form distributions.

Lactoferrin is an iron-binding glycoprotein found in exocrine secretions of mammals and released from neutrophilic granules during inflammation. This review describes the biological roles of lactoferrin in host defence. Secreted lactoferrin exerts antimicrobial action either by chelation of iron or by destabilization of bacterial membranes. Furthermore, lactoferrin modulates the inflammatory process, mainly by preventing the release of cytokines from monocytes and by regulating the proliferation and differentiation of immune cells. Some of these activities are related to the ability of lactoferrin to bind lipopolysaccharides (LPS) with high affinity. Indeed, recent in vitro studies indicate that lactoferrin is able to compete with the LPS-binding protein for LPS binding and therefore to prevent the transfer of LPS to CD14 present at the surface of monocytes. Moreover, the prophylactic properties of lactoferrin against septicemia in vivo have been demonstrated. Taken as a whole, these observations strongly suggest that lactoferrin is one of the key molecules which modulate the inflammatory response.

Human IgG is the most abundant glycoprotein in serum and is crucial for protective immunity. In addition to conserved IgG Fc glycans, ∼15-25% of serum IgG contains glycans within the variable domains. These so-called "Fab glycans" are primarily highly processed complex-type biantennary N-glycans linked to N-glycosylation sites that emerge during somatic hypermutation. Specific patterns of Fab glycosylation are concurrent with physiological and pathological conditions, such as pregnancy and rheumatoid arthritis. With respect to function, Fab glycosylation can significantly affect stability, half-life, and binding characteristics of Abs and BCRs. Moreover, Fab glycans are associated with the anti-inflammatory activity of IVIgs. Consequently, IgG Fab glycosylation appears to be an important, yet poorly understood, process that modulates immunity.

The animal sialyltransferases are Golgi type II transmembrane glycosyltransferases. Twenty distinct sialyltransferases have been identified in both human and murine genomes. These enzymes catalyze transfer of sialic acid from CMP-Neu5Ac to the glycan moiety of glycoconjugates. Despite low overall identities, they share four conserved peptide motifs [L (large), S (small), motif III, and motif VS (very small)] that are hallmarks for sialyltransferase identification. We have identified 155 new putative genes in 25 animal species, and we have exploited two lines of evidence: (1) sequence comparisons and (2) exon-intron organization of the genes. An ortholog to the ancestor present before the split of ST6Gal I and II subfamilies was detected in arthropods. An ortholog to the ancestor present before the split of ST6GalNAc III, IV, V, and VI subfamilies was detected in sea urchin. An ortholog to the ancestor present before the split of ST3Gal I and II subfamilies was detected in ciona, and an ortholog to the ancestor of all the ST8Sia was detected in amphioxus. Therefore, single examples of the four families (ST3Gal, ST6Gal, ST6GalNAc, and ST8Sia) have appeared in invertebrates, earlier than previously thought, whereas the four families were all detected in bony fishes, amphibians, birds, and mammals. As previously hypothesized, sequence similarities among sialyltransferases suggest a common genetic origin, by successive duplications of an ancestral gene, followed by divergent evolution. Finally, we propose predictions on these invertebrates sialyltransferase-related activities that have not previously been demonstrated and that will ultimately need to be substantiated by protein expression and enzymatic activity assays.

All plants and green algae synthesize starch through the action of the same five classes of elongation enzymes: the starch synthases. Arabidopsis mutants defective for the synthesis of the soluble starch synthase IV (SSIV) type of elongation enzyme have now been characterized. The mutant plants displayed a severe growth defect but nonetheless accumulated near to normal levels of polysaccharide storage. Detailed structural analysis has failed to yield any change in starch granule structure. However, the number of granules per plastid has dramatically decreased leading to a large increase in their size. These results, which distinguish the SSIV mutants from all other mutants reported to date, suggest a specific function of this enzyme class in the control of granule numbers. We speculate therefore that SSIV could be selectively involved in the priming of starch granule formation.