We have constructed the first comprehensive microarray representing a human chromosome for analysis of DNA copy number variation. This chromosome 22 array covers 34.7 Mb, representing 1.1% of the genome, with an average resolution of 75 kb. To demonstrate the utility of the array, we have applied it to profile acral melanoma, dermatofibrosarcoma, DiGeorge syndrome and neurofibromatosis 2. We accurately diagnosed homozygous/heterozygous deletions, amplifications/gains, IGLV/IGLC locus instability, and breakpoints of an imbalanced translocation. We further identified the 14-3-3 eta isoform as a candidate tumor suppressor in glioblastoma. Two significant methodological advances in array construction were also developed and validated. These include a strictly sequence defined, repeat-free, and non-redundant strategy for array preparation. This approach allows an increase in array resolution and analysis of any locus; disregarding common repeats, genomic clone availability and sequence redundancy. In addition, we report that the application of phi29 DNA polymerase is advantageous in microarray preparation. A broad spectrum of issues in medical research and diagnostics can be approached using the array. This well annotated and gene-rich autosome contains numerous uncharacterized disease genes. It is therefore crucial to associate these genes to specific 22q-related conditions and this array will be instrumental towards this goal. Furthermore, comprehensive epigenetic profiling of 22q-located genes and high-resolution analysis of replication timing across the entire chromosome can be studied using our array.

Human infertility is a multifactorial disease that affects 8%-12% of reproductive-aged couples worldwide. However, the genetic causes of human infertility are still poorly understood. Synaptonemal complex (SC) is a conserved tripartite structure that holds homologous chromosomes together and plays an indispensable role in the meiotic progression. Here, we identified three homozygous mutations in the SC coding gene C14orf39/SIX6OS1 in infertile individuals from different ethnic populations by whole-exome sequencing (WES). These mutations include a frameshift mutation (c.204_205del [p.His68Glnfs*2]) from a consanguineous Pakistani family with two males suffering from non-obstructive azoospermia (NOA) and one female diagnosed with premature ovarian insufficiency (POI) as well as a nonsense mutation (c.958G>T [p.Glu320*]) and a splicing mutation (c.1180À3C>G) in two unrelated Chinese men (individual P3907 and individual P6032, respectively) with meiotic arrest. Mutations in C14orf39 resulted in truncated proteins that retained SYCE1 binding but exhibited impaired polycomplex formation between C14ORF39 and SYCE1. Further cytological analyses of meiosis in germ cells revealed that the affected familial males with the C14orf39 frameshift mutation displayed complete asynapsis between homologous chromosomes, while the affected Chinese men carrying the nonsense or splicing mutation showed incomplete synapsis. The phenotypes of NOA and POI in affected individuals were well recapitulated by Six6os1 mutant mice carrying an analogous mutation. Collectively, our findings in humans and mice highlight the conserved role of C14ORF39/SIX6OS1 in SC assembly and indicate that the homozygous mutations in C14orf39/SIX6OS1 described here are responsible for infertility of these affected individuals, thus expanding our understanding of the genetic basis of human infertility.

BackgroundIncreasing soil salinization has a detrimental effect on agricultural productivity.Therefore, strategies are needed to induce salinity-tolerance in crop species for sustainable foodproduction. γ-aminobutyric acid (GABA) plays a key role in regulating plant salinity stresstolerance. However, it remains largely unknown how mungbean plants (Vigna radiata L.) respondto exogenous GABA under salinity stress.MethodsThus, we evaluated the effect of exogenous GABA (1.5 mM) on the growth and physiobiochemicalresponse mechanism of mungbean plants to saline stress (0-, 50-, and 100 mM [NaCland Na2SO4, at a 1:1 molar ratio]).ResultsIncreased saline stress adversely affected mungbean plants' growth and metabolism. Forinstance, leaf-stem-root biomass (34- and 56%, 31- and 53%, and 27- and 56% under 50- and 100mM, respectively]) and chlorophyll concentrations declined. The carotenoid level increased (10%)at 50 mM and remained unaffected at 100 mM. Hydrogen peroxide (H2O2), malondialdehyde(MDA), osmolytes (soluble sugars, soluble proteins, proline), total phenolic content, andenzymatic activities of superoxide dismutase (SOD), ascorbate peroxidase (APX), peroxidase(POD), glutathione reductase (GTR), and polyphenol oxidation (PPO) were significantlyincreased. In leaves, salinity caused a significant increase in Na+ concentration but a decrease inK+ concentration, resulting in a low K+/Na+ concentration (51- and 71% under 50- and 100- mMstress). Additionally, nitrogen concentration and the activities of nitrate reductase (NR) andglutamine synthetase (GS) decreased significantly. The reduction in glutamate synthase (GOGAT)activity was only significant (65%) at 100 mM stress. Exogenous GABA decreased Na+, H2O2,and MDA concentrations but enhanced photosynthetic pigments, K+ and K+/Na+ ratio, Nmetabolism, osmolytes, and enzymatic antioxidant activities, thus reducing salinity-associatedstress damages, resulting in improved growth and biomass.ConclusionExogenous GABA may have improved the salinity tolerance of mungbean plants by maintaining their morpho-physiological responses and reducing the accumulation of harmfulsubstances under salinity. Future molecular studies can contribute to a better understanding of themolecular mechanisms by which GABA regulates mungbean salinity tolerance.

Many species of plant-pathogenic gram-negative bacteria deploy the type III (T3) secretion system to secrete virulence components, which are mostly characteristic of protein effectors targeting the cytosol of the plant cell following secretion. Xanthomonas oryzae pv. oryzae (Xoo), a rice pathogen causing bacterial blight disease, uses the T3 accessory protein HrpE to assemble the pilus pathway, which in turn secretes transcription activator-like (TAL) effectors. The hrpE gene can execute extensive physiological and pathological functions beyond effector secretion. As evidenced in this study, when the hrpE gene was deleted from the Xoo genome, the bacteria incur seriouimpairments in multiplication, motility, and virulence. The virulence nullification is attributed to reduced secretion and translocation of PthXo1, which is a TAL effector that determines the bacterial virulence in the susceptible rice varieties. When the HrpE protein produced by prokaryotic expression is applied to plants, the recombinant protein is highly effective at inducing the defense response. Moreover, leaf photosynthesis efficiency is enhanced in HrpE-treated plants. These results provide experimental avenues to modulate the plant defense and growth tradeoff by manipulating a bacterial T3 accessory protein.