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Marine microorganisms have been demonstrated to be an important source for bioactive molecules. In this paper we report the synthesis of Ni nanoparticles (NiSNPs) used as reducing and capping agents for five bacterial strains isolated from an Antarctic marine consortium: Marinomonas sp. ef1, Rhodococcus sp. ef1, Pseudomonas sp. ef1, Brevundimonas sp. ef1, and Bacillus sp. ef1. The NiSNPs were characterized by Ultraviolet-visible (UV-vis) spectroscopy, Dynamic Light Scattering (DLS), Transmission Electron Microscopy (TEM), X-ray diffraction (XRD) and Fourier Transform Infrared (FTIR) spectroscopic analysis. The maximum absorbances in the UV-Vis spectra were in the range of 374 nm to 422 nm, corresponding to the Surface plasmon resonance (SPR) of Nickel. DLS revealed NiSNPs with sizes between 40 and 45 nm. All NiSNPs were polycrystalline with a face-centered cubic lattice, as revealed by XRD analyses. The NiSNPs zeta potential values were highly negative. TEM analysis showed that the NiSNPs were either spherical or rod shaped, well segregated, and with a size between 20 and 50 nm. The FTIR spectra revealed peaks of amino acid and protein binding to the NiSNPs. Finally, all the NiSNPs possess significant antimicrobial activity, which may play an important role in the management of infectious diseases affecting human health.

Robertsonian translocations, specifically rob(1;29) translocation, have reportedly been the most prevalent chromosomal abnormalities in cattle, affecting various breeds and leading to a decrease in fertility and reproductive value. Currently, the identification of rob(1;29) carriers relies on cytogenetic analysis that has limitations in terms of accessibility, cost, and sample requirements. To address these limitations, a novel genomic biomarker was developed in this study for the rapid and precise identification of rob(1;29) carriers. Using q-PCR, a specific copy number variation associated with translocation was targeted, which effectively distinguished between wild-type, homozygous and heterozygous carriers. Crucially, the biomarker can be applied to DNA extracted from various biological matrices, such as semen, embryos, oocytes, milk, saliva, coat, and muscle, and it is compatible with fresh, refrigerated, or frozen samples. Furthermore, this approach offers significant reductions in cost compared to those associated with traditional cytogenetic analysis and provides results within a short turnaround time. The successful development of this genomic biomarker has considerable potential for widespread adoption in screening programs. It facilitates timely identification and management of rob(1;29) carriers while mitigating economic losses and preserving genetic integrity in bovine populations., (© 2024. The Author(s).)

This study presents a novel approach that combines next-generation sequencing (NGS) and cytogenetic technologies for identifying chromosomes involved in chromosomal anomalies. This research focuses on a chromosome anomaly discovered in male Alpine Grey cattle, as well as two previously reported cases of reciprocal translocations (rcps), namely rcp(9;11) and rcp(4;7). Abnormal chromosomes from Alpine Grey cattle were microdissected from conventional preparations, and the amplified products were sequenced using NGS. The sequencing reads were then mapped to the reference genome, and the leverage effect was calculated to identify abnormal reads/Mb values. The result revealed the presence of rob(26;29), which was further confirmed through traditional cytogenetic analyses such as Giemsa staining, CBA-banding, RBA-banding, and FISH techniques. Furthermore, the feasibility of this approach on preserved metaphases was demonstrated through analysis of old slides from previously characterized cases. The study highlights the challenges involved in identifying and characterizing chromosomal aberrations in bovine species and offers a potential solution for analyzing historical anomalies when fresh blood material is unavailable. The combination of NGS and cytogenetic techniques provides a cost-effective and reliable approach for characterizing chromosomal anomalies in various species, including those identified before the availability of modern banding technologies and FISH mapping using specific molecular markers.

One of the most concerning environmental problems is represented by petroleum and its derivatives causing contamination of aquatic and underground environments. In this work, the degradation treatment of diesel using Antarctic bacteria is proposed. Marinomonas sp. ef1 is a bacterial strain isolated from a consortium associated with the Antarctic marine ciliate Euplotes focardii . Its potential in the degradation of hydrocarbons commonly present in diesel oil were studied. The bacterial growth was evaluated in culturing conditions that resembled the marine environment with 1% (v/v) of either diesel or biodiesel added; in both cases, Marinomonas sp. ef1 was able to grow. The chemical oxygen demand measured after the incubation of bacteria with diesel decreased, demonstrating the ability of bacteria to use diesel hydrocarbons as a carbon source and degrade them. The metabolic potential of Marinomonas to degrade aromatic compounds was supported by the identification in the genome of sequences encoding various enzymes involved in benzene and naphthalene degradation. Moreover, in the presence of biodiesel, a fluorescent yellow pigment was produced; this was isolated, purified and characterized by UV-vis and fluorescence spectroscopy, leading to its identification as a pyoverdine. These results suggest that Marinomonas sp. ef1 can be used in hydrocarbon bioremediation and in the transformation of these pollutants in molecules of interest., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

Cr(VI) is highly soluble and mobile in water solution and extremely toxic. In order to obtain a specific material with adsorption properties towards Cr(VI), and that can be used in environmental remediation of water contaminated with Cr(VI), one-step sol-gel technique, at low temperature (50 °C), has been optimized to prepare transparent silica-based xerogel monolith by using tetraethyl orthosilicate as precursor. The obtained xerogel, with disk shape, was fully characterized by Raman, BET, FE-SEM and XRD analysis. The results indicated that the material showed silica amorphous phase and high porosity. The study of the adsorption properties towards different concentrations of Cr(VI), in the form of HCrO 4 - in acidic condition, showed prominent results. The absorption kinetics were evaluated by studying different models, the final result showing that the absorption of Cr(VI) occurred through intra-particle diffusion process, following two steps, and that the absorption equilibrium is regulated by Freundlich isotherm model. The material can be restored by reducing the hazardous Cr(VI) to Cr(III), a less toxic form of chromium, by 1,5-diphenylcarbazide, and with successive treatment in acidic water.

Wine lees are sediments deposited on the walls and bottom of barrels resulting from wine fermentation and mainly consist of yeasts. Saccharomyces cerevisiae extracts, rich in beneficial components for the skin, have already been used in cosmesis, while wine lees have not been well exploited by the cosmetics industry yet. The aim of this work was the full characterization of the wine lees from Verdicchio's wine, with the aim to exploit it as a beneficial ingredient in new cosmetic products. After mapping the microbial composition of the sample waste, the parameters for the sonication extraction process were optimized and the physicochemical properties of the extract were analyzed. The efficiency of the aqueous extraction-and in particular the yeast cell lysis necessary for the release of proteins from the cell-was assessed by evaluating cell shape and size, and protein release, under scanning electron microscopy (SEM), dynamic light scattering (DLS) and Bradford's protein assays. Thus, the total phenol content and antioxidant capacity of the supernatant recovered from native and sonicated lees were determined by Folin-Ciocalteu's and spectrophotometric assays, respectively. To quantify the heavy metals and highlight the presence of microelements beneficial for the skin, inductively coupled plasma-mass spectrometry (ICP-MS) was applied. In vitro metabolic activity and cytotoxicity were tested on both HaCat keratinocytes and human gingival fibroblasts, showing that wine lees are safe for skin's cells. The results show that sonicated lees appear to be more interesting than native ones as a consequence of the release of the active ingredients from the cells. Due to the high antioxidant capacity, content of beneficial elements for skin and an appropriate microbiologic profile, wine lees were included in five new solid cosmetic products and tested for challenge test, compatibility with human skin, sensory analysis, trans epidermal water loss (TEWL) and sebometry.

Poly(ethylene glycol) diacrylate (PEGDA) hydrogels modified with luminescent silver nanoclusters (AgNCs) are synthesized by a photo-crosslinking process. The hybrid material thus obtained is employed to filter Pb(II) polluted water. Under the best conditions, the nanocomposite is able to remove up to 80-90% of lead contaminant, depending on the filter composition. The experimental results indicate that the adsorption process of Pb(II) onto the modified filter can be well modeled using the Freundlich isotherm, thus revealing that the chemisorption is the driving process of Pb(II) adsorption. In addition, the parameter n in the Freundlich model suggests that the adsorption process of Pb(II) ions in the modified hydrogel is favored. Based on the obtained remarkable contaminant uptake capacity and the overall low cost, this hybrid system appears to be a promising sorbent material for the removal of Pb(II) ions from aqueous media.

Metal effects on the gas sensing behavior of metal complexes of 5,10,15,20-tetrakis(4-hydroxyphenyl)porphyrin (THPP) thin film was investigated in terms of detecting NO 2 gas by the planar optical waveguide. For this purpose, several THPP and metal complexes were synthesized with different central metal ions: Co(II), Ni(II), Cu(II), and Zn(II). Planar optical gas sensors were fabricated with the metalloporphyrins deposited on K + ion-exchanged soda-lime glass substrate with the spin coating method serving as host matrices for gas interaction. All of the THPP complex's films were fully characterized by UV-Vis, IR and XPS spectroscopy, and the laser light source wavelength was selected at 520 and 670 nm. The results of the planar optical waveguide sensor show that the Zn-THPP complex exhibits the strongest response with the lowest detectable gas concentration of NO 2 gas for both 520 nm and 670 nm. The Ni-THPP and Co-THPP complexes display good efficiency in the detection of NO 2 , while, on the other hand, Cu-THPP shows a very low interaction with NO 2 gas, with only 50 ppm and 200 ppm detectable gas concentration for 520 nm and 670 nm, respectively. In addition, molecular dynamic simulations and quantum mechanical calculations were performed, proving to be coherent with the experimental results.

Silver nanoparticles (AgNPs) can be used as a surface plasmon resonance (SPR) colorimetric sensor; the correlation between the SPR phenomenon and the aggregation state of nanoparticle allows the real-time detection of a target molecule. Surface functionalization of NPs with proper molecular baits is often performed to establish the selectivity of the sensor. This work reports on the synthesis of AgNPs under reducing conditions and on the functionalization thereof with mercaptoundecanoic acid (11-MUA). UV-VIS Spectroscopy confirmed the formation of AgNPs, eliciting a surface plasmon absorption band (SPAB) at 393 nm that shifted to 417 nm upon surface coating. Dynamic light scattering was used to investigate the surface coatings; moreover, pelleted AgNPs@11MUA nanoparticles were characterized by scanning electron microscopy (SEM), energy dispersive X-ray analyzers (EDX), and infrared spectroscopy to corroborate the presence of 11MUA on the surface. Most interestingly, the resulting AgNPs@11MUA selectively detected micromolar levels of Ni 2+ , also in the presence of other cations such as Mn 2+ , Co 2+ , Cd 2+ , Cu 2+ , Zn 2+ , Fe 2+ , Hg 2+ , Pb 2+ , and Cr 3+ .

The sensing behavior of a thin film composed of metal-free 5, 10, 15, 20-tetrakis (p-hydroxy phenyl) porphyrin and zinc phthalocyanine complex towards m-xylene, styrene, and HCl vapors in a homemade planar optical waveguide (POWG), was studied at room temperature. The thin film was deposited on the surface of potassium ion-exchanged glass substrate, using vacuum spin-coating method, and a semiconductor laser light (532 nm) as the guiding light. Opto-chemical changes of the film exposing with hydrochloric gas, m-xylene, and styrene vapor, were analyzed firstly with UV-Vis spectroscopy. The fabricated POWG shows good correlation between gas exposure response and absorbance change within the gas concentration range 10-1500 ppm. The limit of detection calculated from the logarithmic calibration curve was proved to be 11.47, 21.08, and 14.07 ppm, for HCl gas, m-xylene, and styrene vapors, respectively. It is interesting to find that the film can be recovered to the initial state with trimethylamine vapors after m-xylene, styrene exposures as well as HCl exposure. The gas-film interaction mechanism was discussed considering protonation and π-π stacking with planar aromatic analyte molecules.

In the last decade, metal nanoparticles (NPs) have gained significant interest in the field of biotechnology due to their unique physiochemical properties and potential uses in a wide range of applications. Metal NP synthesis using microorganisms has emerged as an eco-friendly, clean, and viable strategy alternative to chemical and physical approaches. Herein, an original and efficient route for the microbial synthesis of copper NPs using bacterial strains newly isolated from an Antarctic consortium is described. UV-visible spectra of the NPs showed a maximum absorbance in the range of 380-385 nm. Transmission electron microscopy analysis showed that these NPs are all monodispersed, spherical in nature, and well segregated without any agglomeration and with an average size of 30 nm. X-ray powder diffraction showed a polycrystalline nature and face centered cubic lattice and revealed characteristic diffraction peaks indicating the formation of CuONPs. Fourier-transform infrared spectra confirmed the presence of capping proteins on the NP surface that act as stabilizers. All CuONPs manifested antimicrobial activity against various types of Gram-negative; Gram-positive bacteria; and fungi pathogen microorganisms including Escherichia coli , Staphylococcus aureus , and Candida albicans . The cost-effective and eco-friendly biosynthesis of these CuONPs make them particularly attractive in several application from nanotechnology to biomedical science.

Substituent effect on optical gas sensing performance in porphyrin-based optical waveguide detection system was studied by molecular dynamics simulation (MDS), absorption/emission spectrum analysis, and optical waveguide (OWG) detection. The affinities of porphyrin with seven types of substituents (-H, -OH, -tBu, -COOH, -NH 2 , -OCH 3 , -SO 3 - ) on para position of meso-phenyl porphyrin toward gas molecules in adsorption process were studied in different size of boxes with the same pressure and concentration. Analyte gases (CO 2 , H 2 S, HCl, NO 2 ) were exposed to porphyrin film in absorption spectrophotometer, and in OWG with evanescent field excited by a guiding laser light with 670 nm wavelength. The extent of interaction between host molecule and the guest analytes was analyzed by the number of gas molecules in vicinity of 0.3 nm around substituents of porphyrin molecules. Optical waveguide results reveal that sulfonate porphyrin is mostly responsive to hydrochloride, hydrosulfide gas and nitrogen dioxide gases with strong response intensity. Molecular dynamics and spectral analysis provide objective information about the molecular state and sensing properties. Molecular rearrangements induced by gas exposure was studied by spectral analysis and surface morphology before and after gas exposure taking hydrosulfide gas as an example. Film-gas interaction mechanism was discussed in terms of each gas and substituent group characters.

The purpose of this work was the optimization of the extraction from spent coffee grounds, specifically 100% Arabica coffee blends, using a desirability approach. Spent coffees were recovered after the preparation of the espresso coffee under the typical conditions used in coffee bars with a professional machine. Spent coffee was subjected to different extraction procedures in water: by changing the extraction temperature (60, 80, or 100 °C) and the solvent extraction volume (10, 20, 30 mL for 1 gram of coffee) and by maintaining constant the extraction time (30 minutes). The ranges of the process parameters, as well as the solvent to be used, were established by running preliminary experiments not reported here. The variables of interest for the experimental screening design were the content of caffeine, trigonelline, and nicotinic acid, quantitatively determined from regression lines of standard solutions of known concentrations by a validated HPLC-VWD method. Since solvent extraction volumes and temperatures were revealed to be the most significant process variables, for the optimization of the extraction process, an approach based on Response Surface Methodology (RSM) was considered. In particular, a Box-Wilson Central Composite Design, commonly named central composite design (CCD), was used to find the optimal conditions of the extraction process. Moreover, the desirability approach was then applied to maximize the extraction efficiency by searching the optimal values (or at least the best compromise solution) for all three response variables simultaneously. Successively, the best extract, obtained in a volume of 20 mL of water at an extraction temperature of 80 °C, was analyzed for total phenol content (TPC) through the Folin-Ciocalteu assay, and the antioxidant capacities (AC) through the trolox equivalent (TE) antioxidant capacity (DPPH), ferric-ion reducing antioxidant parameter (FRAP), and radical cation scavenging activity and reducing power (ABTS). The TPC and the AC for spent coffee were high and comparable to the results obtained in previous similar studies. Then, the extract was evaluated by inductively coupled plasma mass spectrometry (ICP-MS), revealing that potassium was the most abundant element, followed by phosphorus, magnesium, calcium, sodium, and sulfur, while very low content in heavy metals was observed. Preliminary in vitro assays in keratinocyte HaCaT cells were carried out to assess the safety, in terms of cytotoxicity of spent coffee, and results showed that cell viability depends on the extract concentration: cell viability is unmodified up to a concentration of 0.3 mg/mL, over which it becomes cytotoxic for the cells. Spent coffee extract at 0.03 and 0.3 mg/mL showed the ability to reduce intracellular reactive oxygen species formation induced by hydrogen peroxide in HaCaT cells, suggesting its antioxidant activity at intracellular levels.

Increasing evidence implicates mitochondrial dysfunction in the etiology of Parkinson's disease (PD). Mitochondrial DNA (mtDNA) mutations are considered a possible cause and this mechanism might be shared with the aging process and with other age-related neurodegenerative disorders such as Alzheimer's disease (AD). We have recently proposed a computerized method for mutated mtDNA characterization able to discriminate between AD and aging. The present study deals with mtDNA mutation-based profiling of PD. Peripheral blood mtDNA sequences from late-onset PD patients and age-matched controls were analyzed and compared to the revised Cambridge Reference Sequence (rCRS). The chaos game representation (CGR) method, modified to visualize heteroplasmic mutations, was used to display fractal properties of mtDNA sequences and fractal lacunarity analysis was applied to quantitatively characterize PD based on mtDNA mutations. Parameter β, from the hyperbola model function of our lacunarity method, was statistically different between PD and control groups when comparing mtDNA sequence frames corresponding to GenBank np 5713-9713. Our original method, based on CGR and lacunarity analysis, represents a useful tool to analyze mtDNA mutations. Lacunarity parameter β is able to characterize individual mutation profile of mitochondrial genome and could represent a promising index to discriminate between PD and aging.

The effect of surface modification using ascorbic acid as a surface modifier of nano-TiO₂ heterogeneous photocatalyst was studied. The preparation of supported photocatalyst was made by a specific paste containing ascorbic acid modified TiO₂ nanoparticles used to cover Polypropylene as a support material. The obtained heterogeneous photocatalyst was thoroughly characterized (scanning electron microscope (SEM), RAMAN, X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), photoluminescence (PL), and Diffuse Reflectance Spectra (DRS) and successfully applied in the visible light photodegradation of Alizarin Red S in water solutions. In particular, this new supported TiO₂ photocatalyst showed a change in the adsorption mechanism of dye with respect to that of only TiO₂ due to the surface properties. In addition, an improvement of photocatalytic performances in the visible light photodegration was obtained, showing a strict correlation between efficiency and energy band gap values, evidencing the favorable surface modification of TiO₂ nanoparticles.

The composition of sedimentary pigments in the Antarctic lake at Edmonson Point has been investigated and compared with the aim to provide a useful analytical method for pigments separation and identification, providing reference data for future assessment of possible changes in environmental conditions. Reversed phase high performance liquid chromatography (HPLC) with electrospray-mass spectrometry (ESI-MS) detection and diode array detection (DAD) has been used to identify light screening and light harvesting pigments. The results are discussed in terms of local environmental conditions.

Robertsonian translocation (rob) involving chromosomes 1 and 29 represents the most frequent chromosome abnormality observed in cattle breeds intended for meat production. The negative effects of this anomaly on fertility are widely demonstrated, and in many countries, screening programs are being carried out to eliminate carriers from reproduction. Although rob(1;29) was first observed in 1964, the genomic structure of this anomaly is partially unclear. In this work, we demonstrate that, during the fusion process, around 5.4 Mb of the pericentromeric region of BTA29 moves to the q arm, close to the centromere, of rob(1;29). We also clearly show that this fragment is inverted. We find that no deletion/duplication involving sequences reported in the BosTau6 genome assembly occurred during the fusion process which originates this translocation.

Background: All standard methods for cDNA cloning are affected by a potential inability to effectively clone the 5' region of mRNA. The aim of this work was to estimate mRNA open reading frame (ORF) 5' region sequence completeness in the model organism Danio rerio (zebrafish)., Results: We implemented a novel automated approach (5'_ORF_Extender) that systematically compares available expressed sequence tags (ESTs) with all the zebrafish experimentally determined mRNA sequences, identifies additional sequence stretches at 5' region and scans for the presence of all conditions needed to define a new, extended putative ORF. Our software was able to identify 285 (3.3%) mRNAs with putatively incomplete ORFs at 5' region and, in three example cases selected (selt1a, unc119.2, nppa), the extended coding region at 5' end was cloned by reverse transcription-polymerase chain reaction (RT-PCR)., Conclusion: The implemented method, which could also be useful for the analysis of other genomes, allowed us to describe the relevance of the "5' end mRNA artifact" problem for genomic annotation and functional genomic experiment design in zebrafish.

Background: CYYR1 is a recently identified gene located on human chromosome 21 whose product has no similarity to any known protein and is of unknown function. Analysis of expressed sequence tags (ESTs) have revealed high human CYYR1 expression in cells belonging to the diffuse neuroendocrine system (DNES). These cells may be the origin of neuroendocrine (NE) tumors. The aim of this study was to conduct an initial analysis of sequence, splicing and expression of the CYYR1 mRNA in human NE tumors., Methods: The CYYR1 mRNA coding sequence (CDS) was studied in 32 NE tumors by RT-PCR and sequence analysis. A subtle alternative splicing was identified generating two isoforms of CYYR1 mRNA differing in terms of the absence (CAG- isoform, the first described mRNA for CYYR1 locus) or the presence (CAG+ isoform) of a CAG codon. When present, this specific codon determines the presence of an alanine residue, at the exon 3/exon 4 junction of the CYYR1 mRNA. The two mRNA isoform amounts were determined by quantitative relative RT-PCR in 29 NE tumors, 2 non-neuroendocrine tumors and 10 normal tissues. A bioinformatic analysis was performed to search for the existence of the two CYYR1 isoforms in other species., Results: The CYYR1 CDS did not show differences compared to the reference sequence in any of the samples, with the exception of an NE tumor arising in the neck region. Sequence analysis of this tumor identified a change in the CDS 333 position (T instead of C), leading to the amino acid mutation P111S. NE tumor samples showed no significant difference in either CYYR1 CAG- or CAG+ isoform expression compared to control tissues. CYYR1 CAG- isoform was significantly more expressed than CAG+ isoform in NE tumors as well as in control samples investigated. Bioinformatic analysis revealed that only the genomic sequence of Pan troglodytes CYYR1 is consistent with the possible existence of the two described mRNA isoforms., Conclusion: A new "subtle" splicing isoform (CAG+) of CYYR1 mRNA, the sequence and the expression of this gene were defined in a large series of NE tumors.

Unlabelled: UniGene Tabulator 1.0 provides a solution for full parsing of UniGene flat file format; it implements a structured graphical representation of each data field present in UniGene following import into a common database managing system usable in a personal computer. This database includes related tables for sequence, protein similarity, sequence-tagged site (STS) and transcript map interval (TXMAP) data, plus a summary table where each record represents a UniGene cluster. UniGene Tabulator enables full local management of UniGene data, allowing parsing, querying, indexing, retrieving, exporting and analysis of UniGene data in a relational database form, usable on Macintosh (OS X 10.3.9 or later) and Windows (2000, with service pack 4, XP, with service pack 2 or later) operating systems-based computers., Availability: The current release, including both the FileMaker runtime applications, is freely available at http://apollo11.isto.unibo.it/software/

Background: Formal description of a cell's genetic information should provide the number of DNA molecules in that cell and their complete nucleotide sequences. We pose the formal problem: can the genome sequence forming the genotype of a given living cell be known with absolute certainty so that the cell's behaviour (phenotype) can be correlated to that genetic information? To answer this question, we propose a series of thought experiments., Results: We show that the genome sequence of any actual living cell cannot physically be known with absolute certainty, independently of the method used. There is an associated uncertainty, in terms of base pairs, equal to or greater than micros (where micro is the mutation rate of the cell type and s is the cell's genome size)., Conclusion: This finding establishes an "uncertainty principle" in genetics for the first time, and its analogy with the Heisenberg uncertainty principle in physics is discussed. The genetic information that makes living cells work is thus better represented by a probabilistic model rather than as a completely defined object.

The amino acid sequence of gene products is routinely deduced from the nucleotide sequence of the relative cloned cDNA, according to the rules for recognition of start codon (first-AUG rule, optimal sequence context) and the genetic code. From this prediction stem most subsequent types of product analysis, although all standard methods for cDNA cloning are affected by a potential inability to effectively clone the 5' region of mRNA. Revision by bioinformatics and cloning methods of 109 known genes located on human chromosome 21 (HC 21) shows that 60 mRNAs lack any in-frame stop upstream of the first-AUG, and that in five cases (DSCR1, KIAA0184, KIAA0539, SON, and TFF3) the coding region at the 5' end was incompletely characterized in the original descriptions. We describe the respective consequences for genomic annotation, domain and ortholog identification, and functional experiments design. We have also analyzed the sequences of 13,124 human mRNAs (RefSeq databank), discovering that in 6448 cases (49%), an in-frame stop codon is present upstream of the initiation codon, while in the other 6676 mRNAs (51%), identification of additional bases at the mRNA 5' region could well reveal some new upstream in-frame AUG codons in the optimal context. Proportionally to the HC 21 data, about 550 known human genes might thus be affected by this 5' end mRNA artifact.

A novel human gene has been identified by in-depth bioinformatics analysis of chromosome 21 segment 40/105 (21q21.1), with no coding region predicted in any previous analysis. Brain-derived DNA complementary to RNA (cDNA) sequencing predicts a 154-amino acid product with no similarity to any known protein. The gene has been named cysteine and tyrosine-rich protein 1 gene (symbol cysteine and tyrosine-rich 1, CYYR1). The CYYR1 messenger RNA was found by Northern blot analysis in a broad range of tissues (two transcripts of 3.4 and 2.2 kb). The gene consists of four exons and spans about 107 kb, including a very large intron of 85.8 kb. Analysis of expressed sequence tags shows high CYYR1 expression in cells belonging to the amine precursor uptake and decarboxylation system. We also cloned the cDNA of the murine ortholog Cyyr1, which was mapped by a radiation hybrid panel on chromosome 16 within the region corresponding to that containing the respective human homolog on chromosome 21. Sequence and phylogenetic analysis led to identification of several genes encoding CYYR1 homologous proteins. The most prominent feature identified in the protein family is a central, unique cysteine and tyrosine-rich domain, which is strongly conserved from lower vertebrates (fishes) to humans but is absent in bacteria and invertebrates.

A new gene family has been identified on the basis of in-depth bioinformatics analysis of the Down syndrome candidate region 1 (DSCR1) gene, located on 21q22.1. We have determined the complete coding sequences of similar genes in Saccharomyces cerevisiae and Caenorhabditis elegans, as well as that of a novel human gene, named DSCR1L2 (DSCR1-like 2). Peripheral blood leukocyte cDNA sequencing predicts as its product a 241-amino-acid protein highly similar to products of the human genes DSCR1 and ZAKI-4 (HGMW-approved symbol DSCR1L1). The highest level of expression of DSCR1L2 mRNA was found by Northern blot analysis in heart and skeletal muscles, liver, kidney, and peripheral blood leukocytes (three transcripts of 3.2, 5. 2, and 7.5 kb). The gene consists of four exons and spans about 22 kb on chromosome 1 (1p33-p35.3) (Human Chromosome 1, Sanger Centre). Exon/intron organization is highly conserved between DSCR1 and DSCR1L2. Two alternative DSCR1L2 mRNA splicing forms have been recognized, with one lacking 10 amino acids in the middle of the protein. Analysis of expressed sequence tags (ESTs) shows DSCR1L2 expression in fetal tissues (heart, liver, and spleen) and in adenocarcinomas. ESTs related to the murine DSCR1L2 orthologue are found in the 2-cell stage mouse embryo, in developing brain stem and spinal cord, and in thymus and T cells. The most prominent feature identified in the protein family is a central short, unique serine-proline motif (including an ISPPXSPP box), which is strongly conserved from yeast to human but is absent in bacteria. Moreover, homology with the RNA-binding domain was weakly but consistently detected in a stretch of 80 amino acids at the amino-terminus by fine sequence analysis based on tools utilizing both hidden Markov models and BLAST. The identification of this new gene family should allow a better understanding of the functions of the genes belonging to it., (Copyright 2000 Academic Press.)