SPECC1L: a cytoskeletal protein that regulates embryonic tissue dynamics

Many structural birth defects occur due to failure of tissue movement and fusion events during embryogenesis. Examples of such birth defects include failure of closure of the neural tube, palate, and ventral body wall. Actomyosin forces play a pivotal role in these closure processes, making proteins that regulate actomyosin dynamics a priority when studying the etiology of structural birth defects. SPECC1L (sperm antigen with calponin homology and coiled-coil domains 1 like) cytoskeletal protein associates with microtubules, filamentous actin, non-muscle myosin II (NMII), as well as membrane-associated components of adherens junctions. Patients with SPECC1L mutations show a range of structural birth defects affecting craniofacial development (hypertelorism, cleft palate), ventral body wall (omphalocele), and internal organs (diaphragmatic hernia, bicornuate uterus). Characterization of mouse models indicates that these syndromic mutations utilize a gain-of-function mechanism to affect intra- and supra-cellular actin organization. Interestingly, SPECC1L deficiency appears to affect the efficiency of tissue dynamics, making it an important cytoskeletal regulator to study tissue movement and fusion events during embryonic development. Here we summarize the SPECC1L-related syndrome mutations, phenotypes of Specc1l mouse models, and cellular functions of SPECC1L that highlight how it may regulate embryonic tissue dynamics.

TWIST1 interacts with β/δ-catenins during neural tube development and regulates fate transition in cranial neural crest cells

Cell fate determination is a necessary and tightly regulated process for producing different cell types and structures during development. Cranial neural crest cells (CNCCs) are unique to vertebrate embryos and emerge from the neural plate borders into multiple cell lineages that differentiate into bone, cartilage, neurons and glial cells. We have previously reported that Irf6 genetically interacts with Twist1 during CNCC-derived tissue formation. Here, we have investigated the mechanistic role of Twist1 and Irf6 at early stages of craniofacial development. Our data indicate that TWIST1 is expressed in endocytic vesicles at the apical surface and interacts with β/δ-catenins during neural tube closure, and Irf6 is involved in defining neural fold borders by restricting AP2α expression. Twist1 suppresses Irf6 and other epithelial genes in CNCCs during the epithelial-to-mesenchymal transition (EMT) process and cell migration. Conversely, a loss of Twist1 leads to a sustained expression of epithelial and cell adhesion markers in migratory CNCCs. Disruption of TWIST1 phosphorylation in vivo leads to epidermal blebbing, edema, neural tube defects and CNCC-derived structural abnormalities. Altogether, this study describes a previously uncharacterized function of mammalian Twist1 and Irf6 in the neural tube and CNCCs, and provides new target genes for Twist1 that are involved in cytoskeletal remodeling.

In-frame deletion of SPECC1L microtubule association domain results in gain-of-function phenotypes affecting embryonic tissue movement and fusion events

Patients with autosomal dominant SPECC1L variants show syndromic malformations, including hypertelorism, cleft palate and omphalocele. These SPECC1L variants largely cluster in the second coiled-coil domain (CCD2), which facilitates association with microtubules. To study SPECC1L function in mice, we first generated a null allele (Specc1lΔEx4) lacking the entire SPECC1L protein. Homozygous mutants for these truncations died perinatally without cleft palate or omphalocele. Given the clustering of human variants in CCD2, we hypothesized that targeted perturbation of CCD2 may be required. Indeed, homozygotes for in-frame deletions involving CCD2 (Specc1lΔCCD2) resulted in exencephaly, cleft palate and ventral body wall closure defects (omphalocele). Interestingly, exencephaly and cleft palate were never observed in the same embryo. Further examination revealed a narrower oral cavity in exencephalic embryos, which allowed palatal shelves to elevate and fuse despite their defect. In the cell, wildtype SPECC1L was evenly distributed throughout the cytoplasm and colocalized with both microtubules and filamentous actin. In contrast, mutant SPECC1L-ΔCCD2 protein showed abnormal perinuclear accumulation with diminished overlap with microtubules, indicating that SPECC1L used microtubule association for trafficking in the cell. The perinuclear accumulation in the mutant also resulted in abnormally increased actin and non-muscle myosin II bundles dislocated to the cell periphery. Disrupted actomyosin cytoskeletal organization in SPECC1L CCD2 mutants would affect cell alignment and coordinated movement during neural tube, palate and ventral body wall closure. Thus, we show that perturbation of CCD2 in the context of full SPECC1L protein affects tissue fusion dynamics, indicating that human SPECC1L CCD2 variants are gain-of-function.

Isolation and Time-Lapse Imaging of Primary Mouse Embryonic Palatal Mesenchyme Cells to Analyze Collective Movement Attributes

Development of the palate is a dynamic process, which involves vertical growth of bilateral palatal shelves next to the tongue followed by elevation and fusion above the tongue. Defects in this process lead to cleft palate, a common birth defect. Recent studies have shown that palatal shelf elevation involves a remodeling process that transforms the orientation of the shelf from a vertical to a horizontal one. The role of the palatal shelf mesenchymal cells in this dynamic remodeling has been difficult to study. Time-lapse-imaging-based quantitative analysis has been recently used to show that primary mouse embryonic palatal mesenchymal (MEPM) cells can self-organize into a collective movement. Quantitative analyses could identify differences in mutant MEPM cells from a mouse model with palate elevation defects. This paper describes methods to isolate and culture MEPM cells from E13.5 embryos-specifically for time-lapse imaging-and to determine various cellular attributes of collective movement, including measures for stream formation, shape alignment, and persistence of direction. It posits that MEPM cells can serve as a proxy model for studying the role of palatal shelf mesenchyme during the dynamic process of elevation. These quantitative methods will allow investigators in the craniofacial field to assess and compare collective movement attributes in control and mutant cells, which will augment the understanding of mesenchymal remodeling during palatal shelf elevation. Furthermore, MEPM cells provide a rare mesenchymal cell model for investigation of collective cell movement in general.

SPECC1L-deficient primary mouse embryonic palatal mesenchyme cells show speed and directionality defects

Cleft lip and/or palate (CL/P) are common anomalies occurring in 1/800 live-births. Pathogenic SPECC1L variants have been identified in patients with CL/P, which signifies a primary role for SPECC1L in craniofacial development. Specc1l mutant mouse embryos exhibit delayed palatal shelf elevation accompanied by epithelial defects. We now posit that the process of palate elevation is itself abnormal in Specc1l mutants, due to defective remodeling of palatal mesenchyme. To characterize the underlying cellular defect, we studied the movement of primary mouse embryonic palatal mesenchyme (MEPM) cells using live-imaging of wound-repair assays. SPECC1L-deficient MEPM cells exhibited delayed wound-repair, however, reduced cell speed only partially accounted for this delay. Interestingly, mutant MEPM cells were also defective in coordinated cell movement. Therefore, we used open-field 2D cultures of wildtype MEPM cells to show that they indeed formed cell streams at high density, which is an important attribute of collective movement. Furthermore, activation of the PI3K-AKT pathway rescued both cell speed and guidance defects in Specc1l mutant MEPM cells. Thus, we show that live-imaging of primary MEPM cells can be used to assess mesenchymal remodeling defects during palatal shelf elevation, and identify a novel role for SPECC1L in collective movement through modulation of PI3K-AKT signaling.

Physical and chemical indicators of transformations of poultry carcass parts and broiler litter during short term thermophilic composting

Short-term on-site composting of poultry carcasses and broiler litter (BL) is considered as a feasible technology for pathogen elimination during events of mass mortality in poultry houses. However, factors related to mass losses and physical transformation of the poultry carcass, and associated emissions of volatile organic compounds (VOCs) and odors, have not been thoroughly evaluated. This study aims to characterize the degradation of separated carcass parts co-composted with BL and the associated air emissions during 30 days of enclosed composting at 50 °C with constant aeration. The study was carried out in lab-scale simulators using five mixtures containing feathers, rib bones, skins, breast muscles, and hearts and livers, prepared at a 1:2 volumetric ratio (carcass:BL). Dry mass losses reached 59.5, 41.1, 60.8 and 103.5% (based on weight) or 48.4, 29.6, 49.7, and 94.8% (based on CO₂-C and NH₃-N emissions), for rib bones, skins, breast muscles, and hearts and livers, respectively. Visually, most of the carcass parts were degraded, and the typical carcass odor had disappeared by the end of the 30 days. Out of 24 VOCs, dimethyl disulfide (DMDS) and dimethyl trisulfide (DMTS) contributed 80.7-88.3% of the total VOC flux, considering the partial contribution of each part to the emissions involved with the whole carcass. DMDS, DMTS, benzaldehyde, methanethiol, pentanoic acid, and NH₃, contributed 90.5-97.9% of the odor activity values during composting. DMDS/DMTS ratio is suggested as a potential biomarker of stabilization and readiness of the compost for transportation toward further treatment or safe burial.

SPECC1L regulates palate development downstream of IRF6

SPECC1L mutations have been identified in patients with rare atypical orofacial clefts and with syndromic cleft lip and/or palate (CL/P). These mutations cluster in the second coiled-coil and calponin homology domains of SPECC1L and severely affect the ability of SPECC1L to associate with microtubules. We previously showed that gene-trap knockout of Specc1l in mouse results in early embryonic lethality. We now present a truncation mutant mouse allele, Specc1lΔC510, that results in perinatal lethality. Specc1lΔC510/ΔC510 homozygotes showed abnormal palate rugae but did not show cleft palate. However, when crossed with a gene-trap allele, Specc1lcGT/ΔC510 compound heterozygotes showed a palate elevation delay with incompletely penetrant cleft palate. Specc1lcGT/ΔC510 embryos exhibit transient oral epithelial adhesions at E13.5, which may delay shelf elevation. Consistent with oral adhesions, we show periderm layer abnormalities, including ectopic apical expression of adherens junction markers, similar to Irf6 hypomorphic mutants and Arhgap29 heterozygotes. Indeed, SPECC1L expression is drastically reduced in Irf6 mutant palatal shelves. Finally, we wanted to determine if SPECC1L deficiency also contributed to non-syndromic (ns) CL/P. We sequenced 62 Caucasian, 89 Filipino, 90 Ethiopian, 90 Nigerian and 95 Japanese patients with nsCL/P and identified three rare coding variants (p.Ala86Thr, p.Met91Iso and p.Arg546Gln) in six individuals. These variants reside outside of SPECC1L coiled-coil domains and result in milder functional defects than variants associated with syndromic clefting. Together, our data indicate that palate elevation is sensitive to deficiency of SPECC1L dosage and function and that SPECC1L cytoskeletal protein functions downstream of IRF6 in palatogenesis.

A systematic genetic analysis and visualization of phenotypic heterogeneity among orofacial cleft GWAS signals

Phenotypic heterogeneity is a hallmark of complex traits, and genetic studies of such traits may focus on them as a single diagnostic entity or by analyzing specific components. For example, in orofacial clefting (OFC), three subtypes-cleft lip (CL), cleft lip and palate (CLP), and cleft palate (CP) have been studied separately and in combination. To further dissect the genetic architecture of OFCs and how a given associated locus may be contributing to distinct subtypes of a trait we developed a framework for quantifying and interpreting evidence of subtype-specific or shared genetic effects in complex traits. We applied this technique to create a "cleft map" of the association of 30 genetic loci with three OFC subtypes. In addition to new associations, we found loci with subtype-specific effects (e.g., GRHL3 [CP], WNT5A [CLP]), as well as loci associated with two or all three subtypes. We cross-referenced these results with mouse craniofacial gene expression datasets, which identified additional promising candidate genes. However, we found no strong correlation between OFC subtypes and expression patterns. In aggregate, the cleft map revealed that neither subtype-specific nor shared genetic effects operate in isolation in OFC architecture. Our approach can be easily applied to any complex trait with distinct phenotypic subgroups.

RNA sequencing-based transcriptomic profiles of embryonic lens development for cataract gene discovery

Isolated or syndromic congenital cataracts are heterogeneous developmental defects, making the identification of the associated genes challenging. In the past, mouse lens expression microarrays have been successfully applied in bioinformatics tools (e.g., iSyTE) to facilitate human cataract-associated gene discovery. To develop a new resource for geneticists, we report high-throughput RNA sequencing (RNA-seq) profiles of mouse lens at key embryonic stages (E)10.5 (lens pit), E12.5 (primary fiber cell differentiation), E14.5 and E16.5 (secondary fiber cell differentiation). These stages capture important events as the lens develops from an invaginating placode into a transparent tissue. Previously, in silico whole-embryo body (WB)-subtraction-based "lens-enriched" expression has been effective in prioritizing cataract-linked genes. To apply an analogous approach, we generated new mouse WB RNA-seq datasets and show that in silico WB subtraction of lens RNA-seq datasets successfully identifies key genes based on lens-enriched expression. At ≥2 counts-per-million expression, ≥1.5 log₂ fold-enrichment (p < 0.05) cutoff, E10.5 lens exhibits 1401 enriched genes (17% lens-expressed genes), E12.5 lens exhibits 1937 enriched genes (22% lens-expressed genes), E14.5 lens exhibits 2514 enriched genes (31% lens-expressed genes), and E16.5 lens exhibits 2745 enriched genes (34% lens-expressed genes). Biological pathway analysis identified genes associated with lens development, transcription regulation and signaling pathways, among other functional groups. Furthermore, these new RNA-seq data confirmed high expression of established cataract-linked genes and identified new potential regulators in the lens. Finally, we developed new lens stage-specific UCSC Genome Brower annotation tracks and made these publicly accessible through iSyTE ( https://research.bioinformatics.udel.edu/iSyTE/ ) for user-friendly visualization of lens gene expression/enrichment to prioritize genes from high-throughput data from cataract cases.

Using polyethylene sleeves with forced aeration for composting olive mill wastewater pre-absorbed by vegetative waste

Composting in closed polyethylene sleeves with forced aeration may minimize odor emissions, vectors attraction and leachates associated with open windrows. The present study demonstrates the use of this system for composting olive mill wastewater (OMW), the undesired stream associated with the olive milling industry. A polyethylene sleeve of 1.5-m diameter and ca. 20-m long was packed with shredded municipal green waste which was pre-soaked in OMW for 72 h. Process conditions were controlled by means of a programmable logic controller (PLC) equipped with temperature and oxygen sensors. Thermophilic temperatures (>45 °C) were maintained for one month followed by temperatures in the range of 30-40 °C, ca. 20 °C above ambient temperature, for a period of 3.5 months. Oxygen levels were controlled and the system was kept aerobic. Water content gradually decreased with sufficient levels for efficient composting. The finished compost was non-phytotoxic to Cress (Lepidium sativum L.) in a lab bioassay. It was also found suitable as an ingredient in peat, tuff, and coir based growing media, evaluated by plant growth tests with basil and ornamental plants. The viability of this approach for disposing off OMW is much dependent on the liquid absorption capacity of the vegetative waste.

Exome sequencing provides additional evidence for the involvement of ARHGAP29 in Mendelian orofacial clefting and extends the phenotypic spectrum to isolated cleft palate

BACKGROUND

Recent advances in genomics methodologies, in particular the availability of next-generation sequencing approaches have made it possible to identify risk loci throughout the genome, in particular the exome. In the current study, we present findings from an exome study conducted in five affected individuals of a multiplex family with cleft palate only.

METHODS

The GEnome MINIng (GEMINI) pipeline was used to functionally annotate the single nucleotide polymorphisms, insertions and deletions. Filtering methods were applied to identify variants that are clinically relevant and present in affected individuals at minor allele frequencies (≤1%) in the 1000 Genomes Project single nucleotide polymorphism database, Exome Aggregation Consortium, and Exome Variant Server databases. The bioinformatics tool Systems Tool for Craniofacial Expression-Based Gene Discovery was used to prioritize cleft candidates in our list of variants, and Sanger sequencing was used to validate the presence of identified variants in affected and unaffected relatives.

RESULTS

Our analyses approach narrowed the candidates down to the novel missense variant in ARHGAP29 (GenBank: NM_004815.3, NP_004806.3;c.1654T>C [p.Ser552Pro]. A functional assay in zebrafish embryos showed that the encoded protein lacks the activity possessed by its wild-type counterpart, and migration assays revealed that keratinocytes transfected with wild-type ARHGAP29 migrated faster than counterparts transfected with the p.Ser552Pro ARHGAP29 variant or empty vector (control).

CONCLUSION

These findings reveal ARHGAP29 to be a regulatory protein essential for proper development of the face, identifies an amino acid that is key for this, and provides a potential new diagnostic tool.Birth Defects Research 109:27-37, 2017. © 2016 Wiley Periodicals, Inc.

A flexible control system designed for lab-scale simulations and optimization of composting processes

Understanding and optimization of composting processes can benefit from the use of controlled simulators of various scales. The Agricultural Research Organization Composting Simulator (ARO-CS) was recently built and it is flexibly automated by means of a programmable logic controller (PLC). Temperature, carbon dioxide, oxygen and airflow are monitored and controlled in seven 9-l reactors that are mounted into separate 80-l water baths. The PLC program includes three basic heating modes (pre-determined temperature profile, temperature-feedback ("self-heating"), and carbon dioxide-dependent temperature), three basic aeration modes (airflow dependence on temperature, carbon dioxide, or oxygen) and enables all possible combinations among them. This unique high flexibility provides a robust and valuable research tool to explore a wide range of research questions related to the science and engineering of composting. In this article the logic and flexibility of the control system is presented and demonstrated and its potential applications are discussed.

Composting municipal biosolids in polyethylene sleeves with forced aeration: Process control, air emissions, sanitary and agronomic aspects

Composting in polyethylene sleeves with forced aeration may minimize odor emissions, vectors attraction and leachates associated with open windrows. A disadvantage of this technology is the lack of mixing during composting, potentially leading to non-uniform products. In two pilot experiments using biosolids and green waste (1:1; v:v), thermophilic conditions (>45°C) were maintained for two months, with successful control of oxygen levels and sufficient moisture. Emitted odors declined from 1.5-3.8×10⁵ to 5.9×10³-2.3×10⁴ odor units m^-3-air in the first 3weeks of the process, emphasizing the need of odor control primarily during this period. Therefore, composting might be managed in two phases: (i) a closed sleeve for 6-8weeks during which the odor is treated; (ii) an open pile (odor control is not necessary). Reduction of salmonella, E. coli and coliforms was effective initially, meeting the standards of "Class A" biosolids; however, total and fecal coliforms density increased after opening the second sleeve and exceeded the standard of 1000 most probable number (MPN) per g dry matter. Compost maturity was achieved in the open piles following the two sleeves and the final compost was non-phytotoxic and beneficial as a soil additive.

SPECC1L deficiency results in increased adherens junction stability and reduced cranial neural crest cell delamination

Cranial neural crest cells (CNCCs) delaminate from embryonic neural folds and migrate to pharyngeal arches, which give rise to most mid-facial structures. CNCC dysfunction plays a prominent role in the etiology of orofacial clefts, a frequent birth malformation. Heterozygous mutations in SPECC1L have been identified in patients with atypical and syndromic clefts. Here, we report that in SPECC1L-knockdown cultured cells, staining of canonical adherens junction (AJ) components, β-catenin and E-cadherin, was increased, and electron micrographs revealed an apico-basal diffusion of AJs. To understand the role of SPECC1L in craniofacial morphogenesis, we generated a mouse model of Specc1l deficiency. Homozygous mutants were embryonic lethal and showed impaired neural tube closure and CNCC delamination. Staining of AJ proteins was increased in the mutant neural folds. This AJ defect is consistent with impaired CNCC delamination, which requires AJ dissolution. Further, PI3K-AKT signaling was reduced and apoptosis was increased in Specc1l mutants. In vitro, moderate inhibition of PI3K-AKT signaling in wildtype cells was sufficient to cause AJ alterations. Importantly, AJ changes induced by SPECC1L-knockdown were rescued by activating the PI3K-AKT pathway. Together, these data indicate SPECC1L as a novel modulator of PI3K-AKT signaling and AJ biology, required for neural tube closure and CNCC delamination.

Mutations in SPECC1L, encoding sperm antigen with calponin homology and coiled-coil domains 1-like, are found in some cases of autosomal dominant Opitz G/BBB syndrome

BACKGROUND

Opitz G/BBB syndrome is a heterogeneous disorder characterised by variable expression of midline defects including cleft lip and palate, hypertelorism, laryngealtracheoesophageal anomalies, congenital heart defects, and hypospadias. The X-linked form of the condition has been associated with mutations in the MID1 gene on Xp22. The autosomal dominant form has been linked to chromosome 22q11.2, although the causative gene has yet to be elucidated.

METHODS AND RESULTS

In this study, we performed whole exome sequencing on DNA samples from a three-generation family with characteristics of Opitz G/BBB syndrome with negative MID1 sequencing. We identified a heterozygous missense mutation c.1189A>C (p.Thr397Pro) in SPECC1L, located at chromosome 22q11.23. Mutation screening of an additional 19 patients with features of autosomal dominant Opitz G/BBB syndrome identified a c.3247G>A (p.Gly1083Ser) mutation segregating with the phenotype in another three-generation family.

CONCLUSIONS

Previously, SPECC1L was shown to be required for proper facial morphogenesis with disruptions identified in two patients with oblique facial clefts. Collectively, these data demonstrate that SPECC1L mutations can cause syndromic forms of facial clefting including some cases of autosomal dominant Opitz G/BBB syndrome and support the original linkage to chromosome 22q11.2.

THPO-MPL pathway and bone marrow failure

Single or multilineage bone marrow failure can be a serious health problem caused by hereditary and non-hereditary causes such as exposure to drugs or environmental toxins. Normal hematopoiesis requires the integrity of several pathways including the THPO-MPL pathway. Over the last two decades, significant advances in the understanding of normal and abnormal functions of this and related pathways have led to novel diagnostic and therapeutic options.

Msx1 and Tbx2 antagonistically regulate Bmp4 expression during the bud-to-cap stage transition in tooth development

Bmp4 expression is tightly regulated during embryonic tooth development, with early expression in the dental epithelial placode leading to later expression in the dental mesenchyme. Msx1 is among several transcription factors that are induced by epithelial Bmp4 and that, in turn, are necessary for the induction and maintenance of dental mesenchymal Bmp4 expression. Thus, Msx1(-/-) teeth arrest at early bud stage and show loss of Bmp4 expression in the mesenchyme. Ectopic expression of Bmp4 rescues this bud stage arrest. We have identified Tbx2 expression in the dental mesenchyme at bud stage and show that this can be induced by epithelial Bmp4. We also show that endogenous Tbx2 and Msx1 can physically interact in mouse C3H10T1/2 cells. In order to ascertain a functional relationship between Msx1 and Tbx2 in tooth development, we crossed Tbx2 and Msx1 mutant mice. Our data show that the bud stage tooth arrest in Msx1(-/-) mice is partially rescued in Msx1(-/-);Tbx2(+/-) compound mutants. This rescue is accompanied by formation of the enamel knot (EK) and by restoration of mesenchymal Bmp4 expression. Finally, knockdown of Tbx2 in C3H10T1/2 cells results in an increase in Bmp4 expression. Together, these data identify a novel role for Tbx2 in tooth development and suggest that, following their induction by epithelial Bmp4, Msx1 and Tbx2 in turn antagonistically regulate odontogenic activity that leads to EK formation and to mesenchymal Bmp4 expression at the key bud-to-cap stage transition.

Protein inhibitors of activated STAT (Pias1 and Piasy) differentially regulate pituitary homeobox 2 (PITX2) transcriptional activity

Protein inhibitors of activated STAT (Pias) proteins can act independent of sumoylation to modulate the activity of transcription factors and Pias proteins interacting with transcription factors can either activate or repress their activity. Pias proteins are expressed in many tissues and cells during development and we asked if Pias proteins regulated the pituitary homeobox 2 (PITX2) homeodomain protein, which modulates developmental gene expression. Piasy and Pias1 proteins are expressed during craniofacial/tooth development and directly interact and differentially regulate PITX2 transcriptional activity. Piasy and Pias1 are co-expressed in craniofacial tissues with PITX2. Yeast two-hybrid, co-immunoprecipitation and pulldown experiments demonstrate Piasy and Pias1 interactions with the PITX2 protein. Piasy interacts with the PITX2 C-terminal tail to attenuate its transcriptional activity. In contrast, Pias1 interacts with the PITX2 C-terminal tail to increase PITX2 transcriptional activity. The E3 ligase activity associated with the RING domain in Piasy is not required for the attenuation of PITX2 activity, however, the RING domain of Pias1 is required for enhanced PITX2 transcriptional activity. Bimolecular fluorescence complementation assays reveal PITX2 interactions with Piasy and Pias1 in the nucleus. Piasy represses the synergistic activation of PITX2 with interacting co-factors and Piasy represses Pias1 activation of PITX2 transcriptional activity. In contrast, Pias1 did not affect the synergistic interaction of PITX2 with transcriptional co-factors. Last, we demonstrate that Pias proteins form a complex with PITX2 and Lef-1, and PITX2 and β-catenin. Lef-1, β-catenin, and Pias interactions with PITX2 provide new molecular mechanisms for the regulation of PITX2 transcriptional activity and the activity of Pias proteins.

Effects of harvest date, irrigation level, cultivar type and fruit water content on olive mill wastewater generated by a laboratory scale 'Abencor' milling system

Olive mill wastewaters (OMW) were obtained at laboratory scale by milling olives from four cultivars grown at different irrigation levels and harvested at different times. Samples were compared based on wastewater quantity, pH, suspended matter, salinity, organic load, total phenols, NPK, and phytotoxicity. Principal component analysis discriminated between harvest times, regardless of olive cultivar, indicating substantial influence of fruit ripeness on OMW characteristics. OMW properties were affected both by the composition and the extraction efficiency of fruit water. As the fruit water content increased, the concentrations of solutes in the fruit water decreased, but the original fruit water composed a larger portion of the total wastewater volume. These contradicting effects resulted in lack of correlation between fruit water content and OMW properties. The significant effects shown for fruit ripeness, irrigation and cultivar on OMW characteristics indicate that olive horticultural conditions should be considered in future OMW management.

The cell adhesion gene PVRL3 is associated with congenital ocular defects

We describe a male patient (patient DGAP113) with a balanced translocation, 46,XY,t(1;3)(q31.3;q13.13), severe bilateral congenital cataracts, CNS abnormalities and mild developmental delay. Fluorescence in situ hybridization (FISH) and suppression PCR demonstrated that the chromosome 3 breakpoint lies ~515 kb upstream of the PVRL3 gene, while the chromosome 1 breakpoint lies ~50 kb upstream of the NEK7 gene. Despite the fact that NEK7 is closer to a translocation breakpoint than PVRL3, NEK7 transcript levels are unaltered in patient DGAP113 lymphoblastoid cells and Nek7-deficient mice exhibit no detectable ocular phenotype. In contrast, the expression of PVRL3, which encodes the cell adhesion protein Nectin 3, is significantly reduced in patient DGAP113 lymphoblastoid cells, likely due to a position effect caused by the chromosomal translocation. Nectin 3 is expressed in the mouse embryonic ciliary body and lens. Moreover, Pvrl3 knockout mice as well as a spontaneous mouse mutant ari (anterior retinal inversion), that maps to the Pvrl3 locus, exhibit lens and other ocular defects involving the ciliary body. Collectively, these data identify PVRL3 as a critical gene involved in a Nectin-mediated cell-cell adhesion mechanism in human ocular development.

Deficiency of the cytoskeletal protein SPECC1L leads to oblique facial clefting

Genetic mutations responsible for oblique facial clefts (ObFC), a unique class of facial malformations, are largely unknown. We show that loss-of-function mutations in SPECC1L are pathogenic for this human developmental disorder and that SPECC1L is a critical organizer of vertebrate facial morphogenesis. During murine embryogenesis, Specc1l is expressed in cell populations of the developing facial primordial, which proliferate and fuse to form the face. In zebrafish, knockdown of a SPECC1L homolog produces a faceless phenotype with loss of jaw and facial structures, and knockdown in Drosophila phenocopies mutants in the integrin signaling pathway that exhibit cell-migration and -adhesion defects. Furthermore, in mammalian cells, SPECC1L colocalizes with both tubulin and actin, and its deficiency results in defective actin-cytoskeleton reorganization, as well as abnormal cell adhesion and migration. Collectively, these data demonstrate that SPECC1L functions in actin-cytoskeleton reorganization and is required for proper facial morphogenesis.

Mutations in the RNA granule component TDRD7 cause cataract and glaucoma

The precise transcriptional regulation of gene expression is essential for vertebrate development, but the role of posttranscriptional regulatory mechanisms is less clear. Cytoplasmic RNA granules (RGs) function in the posttranscriptional control of gene expression, but the extent of RG involvement in organogenesis is unknown. We describe two human cases of pediatric cataract with loss-of-function mutations in TDRD7 and demonstrate that Tdrd7 nullizygosity in mouse causes cataracts, as well as glaucoma and an arrest in spermatogenesis. TDRD7 is a Tudor domain RNA binding protein that is expressed in lens fiber cells in distinct TDRD7-RGs that interact with STAU1-ribonucleoproteins (RNPs). TDRD7 coimmunoprecipitates with specific lens messenger RNAs (mRNAs) and is required for the posttranscriptional control of mRNAs that are critical to normal lens development and to RG function. These findings demonstrate a role for RGs in vertebrate organogenesis.

Apc inhibition of Wnt signaling regulates supernumerary tooth formation during embryogenesis and throughout adulthood

The ablation of Apc function or the constitutive activation of beta-catenin in embryonic mouse oral epithelium results in supernumerary tooth formation, but the underlying mechanisms and whether adult tissues retain this potential are unknown. Here we show that supernumerary teeth can form from multiple regions of the jaw and that they are properly mineralized, vascularized, innervated and can start to form roots. Even adult dental tissues can form new teeth in response to either epithelial Apc loss-of-function or beta-catenin activation, and the effect of Apc deficiency is mediated by beta-catenin. The formation of supernumerary teeth via Apc loss-of-function is non-cell-autonomous. A small number of Apc-deficient cells is sufficient to induce surrounding wild-type epithelial and mesenchymal cells to participate in the formation of new teeth. Strikingly, Msx1, which is necessary for endogenous tooth development, is dispensable for supernumerary tooth formation. In addition, we identify Fgf8, a known tooth initiation marker, as a direct target of Wnt/beta-catenin signaling. These studies identify key mechanistic features responsible for supernumerary tooth formation.

Characterization of apparently balanced chromosomal rearrangements from the developmental genome anatomy project

Apparently balanced chromosomal rearrangements in individuals with major congenital anomalies represent natural experiments of gene disruption and dysregulation. These individuals can be studied to identify novel genes critical in human development and to annotate further the function of known genes. Identification and characterization of these genes is the goal of the Developmental Genome Anatomy Project (DGAP). DGAP is a multidisciplinary effort that leverages the recent advances resulting from the Human Genome Project to increase our understanding of birth defects and the process of human development. Clinically significant phenotypes of individuals enrolled in DGAP are varied and, in most cases, involve multiple organ systems. Study of these individuals' chromosomal rearrangements has resulted in the mapping of 77 breakpoints from 40 chromosomal rearrangements by FISH with BACs and fosmids, array CGH, Southern-blot hybridization, MLPA, RT-PCR, and suppression PCR. Eighteen chromosomal breakpoints have been cloned and sequenced. Unsuspected genomic imbalances and cryptic rearrangements were detected, but less frequently than has been reported previously. Chromosomal rearrangements, both balanced and unbalanced, in individuals with multiple congenital anomalies continue to be a valuable resource for gene discovery and annotation.

SUMO1 Haploinsufficiency Leads to Cleft Lip and Palate

The posttranslational modification sumoylation can have multiple effects on its substrate proteins. We studied a patient with isolated cleft lip and palate and a balanced chromosomal translocation that disrupts the SUMO1 (small ubiquitin-related modifier) gene, resulting in haploinsufficiency. In mouse, we found that Sumo1 is expressed in the developing lip and palate and that a Sumo1 hypomorphic allele manifests an incompletely penetrant orofacial clefting phenotype. Products of several genes implicated in clefting are sumoylated, and the Sumo1 hypomorphic allele interacts genetically with a loss-of-function allele for one of these loci. Thus, sumoylation defines a network of genes important for palatogenesis.

An unusual class of PITX2 mutations in Axenfeld-Rieger syndrome

BACKGROUND

Mutations in the PITX2 homeobox gene are known to contribute to Axenfeld-Rieger syndrome (ARS), an autosomal-dominant developmental disorder. Although most mutations are in the homeodomain and result in a loss of function, there is a growing subset in the C-terminal domain that has not yet been characterized. These mutations are of particular interest because the C-terminus has both inhibitory and stimulatory activities.

METHODS

In this study we used a combination of in vitro DNA binding and transfection reporter assays to investigate the fundamental issue of whether C-terminal mutations result in gain or loss of function at a cellular level.

RESULTS

We report a new frameshift mutation in the PITX2 allele that predicts a truncated protein lacking most of the C-terminal domain (D122FS). This newly reported mutant and another ARS C-terminal mutant (W133Stop) both have greater binding than wild-type to the bicoid element. Of interest, the mutants yielded approximately 5-fold greater activation of the prolactin promoter in CHO cells, even though the truncated proteins were expressed at lower levels than the wild-type protein. The truncated proteins also had greater than wild-type activity in 2 other cell lines, including the LS8 oral epithelial line that expresses the endogenous Pitx2 gene.

CONCLUSIONS

The results indicate that the PITX2 C-terminal domain has inhibitory activity and support the notion that ARS may also be caused by gain-of-function mutations.

Cell-specific activation of the atrial natriuretic factor promoter by PITX2 and MEF2A

The PITX2 homeodomain protein is mutated in patients with Axenfeld-Rieger syndrome and is involved in the development of multiple organ systems, including the heart. We have examined the interaction of PITX2 isoforms with myocyte-enhancing factor 2A (MEF2A), which is a known regulator of cardiac development. A direct interaction between PITX2a and MEF2A was demonstrated using yeast two-hybrid and GST pull-down assays. To study the functional significance of this interaction, we used the atrial natriuretic factor (ANF) promoter. Coexpression of MEF2A and PITX2a or Pitx2c resulted in a strong synergistic activation of the ANF promoter in LS8 oral epithelial cells but not in other cell lines (NIH/3T3, Chinese hamster ovary, or C2C12). The synergism was dependent on promoter context, because it required MEF2 binding sites and was not seen with two other PITX2 target promoters. DNA binding by MEF2A was required but not sufficient for synergism. Upstream activators of p38 MAP kinases, MKK3 and MKK6, increased PITX2a and Pitx2c activity to yield up to 90-fold activation of the ANF promoter in LS8 cells. Because Axenfeld-Rieger syndrome is autosomal dominant and affects development of the oral epithelium, we tested one of the known PITX2 mutants. The PITX2a-K88E mutant protein suppressed wild type PITX2a synergism with MEF2A. These results demonstrate a promoter- and cell-specific functional interaction between PITX2 and MEF2A and suggest the possibility of coordinate control by these factors in the oral epithelium.

Degradation of 2,4,6-tribromophenol by bacterial cells attached to chalk collected from a contaminated aquifer

AIM

To investigate the factors governing the adhesion and activity of the 2,4,6-tribromophenol (TBP) degrading bacterium Achromobacter piechaudii TBPZ-N61 on chalk from a contaminated aquifer.

METHODS AND RESULTS

Adhesion kinetics of TBPZ-N61 to grey and white chalk from a polluted fractured chalk aquifer was tested in a batch system. Both grey and white chalk contain ca 80% CaCO3, while grey chalk contains more organic matter (2.4%) than the white chalk (0.3%) and also contains Dolmite and Clinoptilolite. Adhesion of the bacterial cells to the chalk particles (<0.2 mm) occurred rapidly (96% of the cells within 15 min). Langmuir-fitted adhesion isotherms suggest that cells in the stationary phase, which are more hydrophobic, adhere to both grey and white chalk more efficiently than cells in the logarithmic growth phase. Increasing the pH (from 6.7 to 8.1) caused a significant reduction in cell adhesion to the chalk. Activity of attached cells was evaluated in both batch and column experiments. Logarithmic cells adhering to white and grey chalk were more active in TBP degradation than cells in suspension. In column experiments, significant TBP degradation was retained up to 30 days after a single injection of TBPZ cells. Thereafter, activity was fully recovered by amendment of yeast extract. Chalk surfaces that were incubated in situ in contaminated groundwater for 20 days still allowed the adhesion and activity of TBPZ cells.

CONCLUSIONS

Taken together, our results show that bacteria adhere efficiently to specific sites on the chalk surfaces, and that sustained bacterial activity of the attached cells can be achieved by adding a carbon source such as yeast extract which also overcome toxic constituents that may occur in some chalk types.

SIGNIFICANCE AND IMPACT OF THE STUDY

Bioremediation of TBP-contaminated chalk aquifers is made possible by the injection of bacterial cultures.

Lymphome angiocentrique de la face : à propos de 2 cas

Angiocentric lymphoma of the face is a rare malignancy. During 11 years, only two patients were treated for a lymphoma of the face. The first patient, 31-year-old, had an angiocentric lymphoma of the nasal cavity, the second patient, 40-year-old, had an angiocentric lymphoma of the nasopharynx and the maxillary sinuses, with an extension the hard palate. According to the Ann Arbor classification, the disease was stage IEab and stage IIEbb, respectively. The first patient was treated by chemotherapy alone (COP regimen) and the second patient underwent combined chemotherapy (CHOP) and radiotherapy. The follow-up was marked by progression of the disease 7 and 9 months after the end of the treatment in the two cases. For the angiocentric lymphoma, treatment based on radiotherapy or chemotherapy alone or combined does not often provide local control and the overall survival rate does not exceed 40% at 5 years.

Dominant negative dimerization of a mutant homeodomain protein in Axenfeld-Rieger syndrome

Axenfeld-Rieger syndrome is an autosomal-dominant disorder caused by mutations in the PITX2 homeodomain protein. We have studied the mechanism underlying the dominant negative K88E mutation, which occurs at position 50 of the homeodomain. By using yeast two-hybrid and in vitro pulldown assays, we have documented that PITX2a can form homodimers in the absence of DNA. Moreover, the K88E mutant had even stronger dimerization ability, primarily due to interactions involving the C-terminal region. Dimerization allowed cooperative binding of wild-type (WT) PITX2a to DNA containing tandem bicoid sites in a head-to-tail orientation (Hill coefficient, 1.73). In contrast, the WT-K88E heterodimer bound the tandem sites with greatly reduced cooperativity and decreased transactivation activity. To further explore the role of position 50 in PITX2a dimerization, we introduced a charge-conservative mutation of lysine to arginine (K88R). The K88R protein had greatly reduced binding to a TAATCC element and did not specifically bind any other TAATNN motif. Like K88E, K88R formed relatively stronger dimers with WT. As predicted by our model, the K88R protein acted in a dominant negative manner to suppress WT PITX2a activity. These results suggest that the position 50 residue in the PITX2 homeodomain plays an important role in both DNA binding and dimerization activities.

Identification of a dominant negative homeodomain mutation in Rieger syndrome

Mutations in the PITX2 bicoid-like homeobox gene cause Rieger syndrome. Rieger syndrome is an autosomal-dominant human disorder characterized by glaucoma as well as dental hypoplasia, mild craniofacial dysmorphism, and umbilical stump abnormalities. PITX2 has also been implicated in the development of multiple organs and left-right asymmetry in the body plan. The PITX2 homeodomain has a lysine at position 50, which has been shown to impart the bicoid-type (TAATCC) DNA binding specificity to other homeodomain proteins. A mutation (K88E), found in a Rieger syndrome patient, changes this lysine to glutamic acid. We were intrigued by the relatively pronounced phenotypic consequences of this K88E mutation. In the initial analyses, the mutant protein appeared to simply be inactive, with essentially no DNA binding and transactivation activities and, unlike the wild type protein, with an inability to synergize with another transcription factor, Pit-1. However, when the K88E DNA was cotransfected with wild type PITX2, analogous to the patient genotype, the K88E mutant suppressed the synergism of wild type PITX2 with Pit-1. In contrast, a different PITX2 homeodomain mutant, T68P, which is also defective in DNA binding, transactivation, and Pit-1 synergism activities, did not suppress the wild type synergism with Pit-1. These results describe the first dominant negative missense mutation in a homeodomain and support a model that may partially explain the phenotypic variation within Rieger syndrome.

Characterization of six novel mutations in the methylenetetrahydrofolate reductase (MTHFR) gene in patients with homocystinuria

Severe deficiency of methylenetetrahydrofolate reductase (MTHFR) is the most common inborn error of folate metabolism. Patients are characterized by severe hyperhomocysteinemia, homocystinuria and a variety of neurological and vascular problems. Eighteen rare mutations have been reported in this group of patients. Two polymorphisms which cause mild enzyme deficiencies have been described (677C-->T and 1298A-->C). The first sequence change encodes a thermolabile enzyme and is associated with mild hyperhomocysteinemia. Six novel point mutations are described in patients with severe deficiency of MTHFR, along with their associated polymorphisms and clinical phenotypes. Of the two nonsense mutations (1762A-->T, 1134C-->G) and four missense mutations (1727C-->T, 1172G-->A, 1768G-->A, and 358G-->A), one was identified in the N-terminal catalytic domain, while the others were located in the regulatory C-terminal region. All four residues affected by missense mutations are conserved in one or more MTHFRs of other species. This report brings the total to 24 mutations identified in severe MTHFR deficiency, with two mutations identified in each of 22 patients.

Molecular genetics of cystinuria: mutation analysis of SLC3A1 and evidence for another gene in type I (silent) phenotype

BACKGROUND

Cystinuria is a hereditary disorder that affects luminal transport of cystine and dibasic amino acids in kidney and small intestine. Three subtypes have been defined on the basis of urinary excretion of cystine in obligate heterozygotes. Mutations in the SLC3A1 gene have been associated with the Type I phenotype.

METHODS

We investigated 20 cystinuria patients from Quebec (8 Type I/I, 9 Type I/III and 3 Type II/N) for mutations in SLC3A1. DNA was studied by Southern blotting and by the single strand conformation polymorphism (SSCP) protocol to identify mutations. Expression of mutations in Xenopus oocytes was performed to confirm the effect of missense mutations on cystine uptake.

RESULTS

Six novel mutations (2 large deletions, a 2 bp deletion and 3 single bp substitutions) were identified on the Type I allele. Four missense mutations (T216M, S217R, R270L and I618M) were expressed in vitro; the first three changes significantly decreased uptake.

CONCLUSIONS

Combined with our previous work, we have identified 15/16 mutations in SLC3A1 on Type I alleles in the eight Type I/I patients, but only one SLC3A1 mutation on the nine Type I alleles of the Type I/III patients. Therefore, we propose that the Type I phenotype could be caused by mutations in other, as yet unidentified cystinuria genes.

Cystinuria subtype and the risk of nephrolithiasis

BACKGROUND

Cystinuria patients may be classified into several subgroups based on the urinary phenotype of heterozygotes. However, the relative risk for nephrolithiasis and the prevalence of SLC3A1 mutations in these subgroups are unknown.

METHODS

Urinary cystine excretion, age at onset of nephrolithiasis and nature of SLC3A1 mutations were assessed prospectively in 23 cystinuria patients identified primarily through the Quebec Newborn Screening Program. Probands were classified as to cystinuria subtype on the basis of parental urinary cystine excretion.

RESULTS

For classical Type I/I cystinuria, both parents excrete cystine in the normal range and probands carry two mutations of the SLC3A1 gene in nearly every case. Between ages 1 to 7 years, mean cystine excretion was high (4566 +/- 480 microns cystine/g creatinine) and exceeded the theoretic threshold for solubility on 70% of visits. Four of eight Type I/I patients began forming stones in the first decade. Type I/III patients (N = 12) excreted less cystine (1544 +/- 163 mumol cystine/g creatinine), exceeded the threshold of urinary cystine solubility less frequently (22% of visits) and had no nephrolithiasis in the first decade; one formed a stone at age 16 years. Only one SLC3A1 mutation was identified in this group. Two Type II/N cystinuria children were identified. In these families, the same level of relatively high excretion (> 600 mumol cystine/g creatinine) was noted in two or three generations, but no SLC3A1 mutations were identified.

CONCLUSIONS

Classical recessive Type I/I cystinuria is genetically and phenotypically distinct from the other subtypes (Type I/III and Type II/N) identified in our population.

Sol-gel applications in environmental biotechnology

Sol gel process was applied for three different applications in environmental biotechnology: (1) thin, fluorescein diacetate-doped sol-gel film made possible epifluorescent microscopic examination of adsorbed Escherichia coli CN13 cells without additional staining: (2) Thiobacillus thiooxidans cell-free extract entrapped into sol-gel matrix displayed oxidative activity on H2S in liquid medium; and (3) two media (E. coli (EC) and sulfate-reducing bacteria (SRB)) were doped into sol-gel and used to enumerate environmental samples for E. coli and sulfate-reducing bacteria, by the most probable number (MPN) method. The comparison of the modified method with the standard enumeration method revealed very good correlation. The sol-gel MPN method is sensitive, saves times, and the substrate can be prepared and stored long-term at room temperature (up to 1 year).